Genes and gene networks underlying spatial cognition in food-caching chickadees

Substantial progress has been made in understanding the genetic architecture of phenotypes involved in a variety of evolutionary processes. Behavioral genetics remains, however, among the least understood. We explore the genetic architecture of spatial cognitive abilities in a wild passerine bird, the mountain chickadee (Poecile gambeli). Mountain chickadees cache thousands of seeds in the fall and require specialized spatial memory to recover these caches throughout the winter. We previously showed that variation in spatial cognition has a direct effect on fitness and has a genetic basis. It remains unknown which specific genes and developmental pathways are particularly important for shaping spatial cognition. To further dissect the genetic basis of spatial cognitive abilities, we combine experimental quantification of spatial cognition in wild chickadees with whole-genome sequencing of 162 individuals, a new chromosome-scale reference genome, and species-specific gene annotation. We have identified a set of genes and developmental pathways that play a key role in creating variation in spatial cognition and found that the mechanism shaping cognitive variation is consistent with selection against mildly deleterious non-coding mutations. Although some candidate genes were organized into connected gene networks, about half do not have shared regulation, highlighting that multiple independent developmental or physiological mechanisms contribute to variation in spatial cognitive abilities. A large proportion of the candidate genes we found are associated with synaptic plasticity, an intriguing result that leads to the hypothesis that certain genetic variants create antagonism between behavioral plasticity and long-term memory, each providing distinct benefits depending on ecological context.

Asymptomatic neonatal herpes simplex virus infection in mice leads to long-term cognitive impairment

Neonatal herpes simplex virus (nHSV) is a devastating infection impacting approximately 14,000 newborns globally each year. Infection is associated with high neurologic morbidity and mortality, making early intervention and treatment critical. Clinical outcomes of symptomatic nHSV infections are well-studied, but little is known about the frequency of, or outcomes following, sub-clinical or asymptomatic nHSV. Given the ubiquitous nature of HSV infection and frequency of asymptomatic shedding in adults, subclinical infections are underreported, yet could contribute to long-term neurological damage. To assess potential neurological morbidity associated with subclinical nHSV infection, we developed a low-dose (100 PFU) HSV infection protocol in neonatal C57BL/6 mice. At this dose, HSV DNA was detected in the brain by PCR but was not associated with acute clinical symptoms. However, months after initial inoculation with 100 PFU of HSV, we observed impaired mouse performance on a range of cognitive and memory performance tasks. Memory impairment was induced by infection with either HSV-1 or HSV-2 wild-type viruses, but not by a viral mutant lacking the autophagy-modulating Beclin-binding domain of the neurovirulence gene γ34.5. Retroviral expression of wild type γ34.5 gene led to behavioral pathology in mice, suggesting that γ34.5 expression may be sufficient to cause cognitive impairment. Maternal immunization and HSV-specific antibody treatment prevented offspring from developing neurological sequelae following nHSV-1 infection. Altogether, these results support the idea that subclinical neonatal infections may lead to cognitive decline in adulthood, with possible profound implications for research on human neurodegenerative disorders such as Alzheimer's Disease.

Survey of rectal cancer MRI technique and reporting tumour descriptors in the UK: a multi-centre British Society of Gastrointestinal and Abdominal Radiology (BSGAR) audit

AIM

To evaluate variation in magnetic resonance imaging (MRI) technique and reporting of rectal cancer staging examinations across the UK.

MATERIALS AND METHODS

A retrospective, multi-centre audit was undertaken of imaging protocols and information documented within consecutive MRI rectal cancer reports between March 2020 and August 2021, which were compared against American and European guidelines. Inclusion criteria included histologically proven rectal adenocarcinoma and baseline staging MRI rectum only.

RESULTS

Fully anonymised data from 924 MRI reports by 78 radiologists at 24 centres were evaluated. Thirty-two per cent of radiologists used template reporting, but these reports offered superior documentation of 13 out of 18 key tumour features compared to free-text reports including T-stage, relation to peritoneal reflection and mesorectal fascia (MRF), nodal status, and presence of extramural venous invasion (EMVI; p<0.027 in each). There was no significant differences in the remaining five features. Across all tumour locations, the tumour relationship to the MRF, the presence of EMVI, and the presence of tumour deposits were reported in 79.5%, 85.6%, and 44% of cases, respectively, and tumour, nodal, and distant metastatic stage documented in 94.4%, 97.7%, and 78.3%. In low rectal tumours, the relationship to the anal sphincter complex was reported in only 54.6%.

CONCLUSION

Considerable variation exists in rectal cancer MRI acquisition and reporting in this sample of UK centres. Inclusion of key radiological features in reports must be improved for risk stratification and treatment decisions. Template reporting is superior to free-text reporting. Routine adoption of standardised radiology practices should now be considered to improve standards to facilitate personalised precision treatment for patients to improve outcomes.

Anthropogenic Change and the Process of Speciation

Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.

Quantitative Analyses of Coupling in Hybrid Zones

In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.

Thermal acclimation in a non-migratory songbird occurs via changes to thermogenic capacity, but not conductance

Thermoregulatory performance can be modified through changes in various subordinate traits, but the rate and magnitude of change in these traits is poorly understood. We investigated flexibility in traits that affect thermal balance between black-capped chickadees (Poecile atricapillus) acclimated for 6 weeks to cold (-5°C) or control (23°C) environments (n=7 per treatment). We made repeated measurements of basal and summit metabolic rates via flow-through respirometry and of body composition using quantitative magnetic resonance of live birds. At the end of the acclimation period, we measured thermal conductance of the combined feathers and skins. Cold-acclimated birds had a higher summit metabolic rate, reflecting a greater capacity for endogenous heat generation, and an increased lean mass. However, birds did not alter their thermal conductance. These results suggest that chickadees respond to cold stress by increasing their capacity for heat production rather than increasing heat retention, an energetically expensive strategy.

The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds

Trait genetic architecture plays an important role in the probability that variation in that trait leads to divergence and speciation. In some cases, speciation may be driven by the generation of novel phenotypes through the recombination of genes associated with traits that are important for local adaptation or sexual selection. Here, we investigate the genetic basis of three plumage color traits, and one ecological trait, breeding elevation, in a recent avian radiation, the North American rosy-finches (Leucosticte spp.). We identify unique genomic regions associated with each trait and highlight 11 candidate genes. Among these are well-characterized melanogenesis genes, including Mitf and Tyrp1, and previously reported hypoxia-related genes including Egln1. Additionally, we use mitochondrial data to date the divergence of rosy-finch clades which appear to have diverged within the past 250 ky. Given the low levels of genome-wide differentiation among rosy-finch taxa, and evidence for extensive introgression in North America, plumage coloration and adaptation to high elevations have likely played large roles in generating the observed patterns of lineage divergence. The relative independence of these candidate regions across the genome suggests that recombination might have led to multiple phenotypes, and subsequent rosy-finch speciation, over short periods of time.

Survey of haemosporidian parasite infections in an endangered high alpine bird

The Brown-capped Rosy-Finch is an endangered high alpine specialist that breeds on cliffs in the Rocky Mountains of North America. We know little about the parasites that infect these birds but filling this knowledge gap is important for understanding their population decline. The aim of this study was to survey haemosporidian parasite infections in Brown-capped Rosy-Finches. We sampled 104 Brown-capped Rosy-Finches during their breeding season at six sampling sites spanning the Colorado Rocky Mountains where they are nearly endemic. We used nested PCR methods to screen birds for parasite infections, and Sanger sequencing data were used to identify parasite lineages. Four of the sampling sites had birds with infections. Females were more often infected than males (prevalence = 15.6% and 9.7%, respectively). We observed twice as many infected birds sampled in July compared to birds sampled in June (prevalence = 12.5% and 6.25%, respectively). The percent of infected birds by sampling site ranged from 0 to over 20%. In total we identified eight different genetic lineages of haemosporidian parasites infecting Brown-capped Rosy-Finches-seven were in the genus Leucocytozoon, and one was in the genus Haemoproteus. Network analysis clearly separates Haemoproteus from Leucocytozoon, with Leucocytozoon lineages comprising two major clusters. Based on reports made to the MalAvi database, all lineages in Cluster 1 have the same reported insect vector, Simulium silvestre. We report that Brown-capped Rosy-Finches experience infections with haemosporidian parasites and that the percentage of infected birds differed markedly between sampling sites. We hypothesize that vector ecology and associated variation in climate at sampling sites explain our observations.

Hybridization between closely related songbirds is related to human habitat disturbance

Human habitat disturbances can promote hybridization between closely related, but typically reproductively isolated, species. We explored whether human habitat disturbances are related to hybridization between two closely related songbirds, black-capped and mountain chickadees, using both genomic and citizen science data sets. First, we genotyped 409 individuals from across both species' ranges using reduced-representation genome sequencing and compared measures of genetic admixture to a composite measure of human landscape disturbance. Then, using eBird observations, we compared human landscape disturbance values for sites where phenotypically diagnosed hybrids were observed to locations where either parental species was observed to determine whether hybrid chickadees are reported in more disturbed areas. We found that hybridization between black-capped and mountain chickadees positively correlates with human habitat disturbances. From genomic data, we found that (1) hybrid index (HI) significantly increased with habitat disturbance, (2) more hybrids were sampled in disturbed habitats, (3) mean HIs were higher in disturbed habitats versus wild habitats, and (4) hybrids were detected in habitats with significantly higher disturbance values than parentals. Using eBird data, we found that both hybrid and black-capped chickadees were significantly more disturbance-associated than mountain chickadees. Surprisingly, we found that nearly every black-capped chickadee we sampled contained some proportion of hybrid ancestry, while we detected very few mountain chickadee backcrosses. Our results highlight that hybridization between black-capped and mountain chickadees is widespread, but initial hybridization is rare (few F1s were detected). We conclude that human habitat disturbances can erode pre-zygotic reproductive barriers between chickadees and that post-zygotic isolation is incomplete. Understanding what becomes of recently hybridizing species following large-scale habitat disturbances is a new, but pressing, consideration for successfully preserving genetic biodiversity in a rapidly changing world.

Sympatry leads to reduced body condition in chickadees that occasionally hybridize

Both abiotic and biotic drivers influence species distributions. Abiotic drivers such as climate have received considerable attention, even though biotic drivers such as hybridization often interact with abiotic drivers. We sought to explore the (1) costs of co‐occurrence for ecologically similar species that hybridize and (2) associations between ecological factors and condition to understand how abiotic and biotic factors influence species distributions. For two closely related and ecologically similar songbirds, black‐capped and mountain chickadees, we characterized body condition, as a proxy for fitness, using a 1358‐individual range‐wide dataset. We compared body condition in sympatry and allopatry with several abiotic and biotic factors using species‐specific generalized linear mixed models. We generated genomic data for a subset of 217 individuals to determine the extent of hybridization‐driven admixture in our dataset. Within this data subset, we found that ~11% of the chickadees had hybrid ancestry, and all hybrid individuals had typical black‐capped chickadee plumage. In the full dataset, we found that birds of both species, independent of demographic and abiotic factors, had significantly lower body condition when occurring in sympatry than birds in allopatry. This could be driven by either the inclusion of cryptic, likely poor condition, hybrids in our full dataset, competitive interactions in sympatry, or range edge effects. We are currently unable to discriminate between these mechanisms. Our findings have implications for mountain chickadees in particular, which will encounter more black‐capped chickadees as black‐capped chickadee ranges shift upslope and could lead to local declines in mountain chickadee populations.

A supergene underlies linked variation in color and morphology in a Holarctic songbird

The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). We demonstrate that variation in redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion. Within this inversion, we find multiple candidate genes related to melanogenesis, carotenoid coloration, and bill shape, suggesting the inversion acts as a supergene controlling multiple linked traits. A latitudinal gradient in ecotype distribution suggests supergene driven variation in color and bill morphology are likely under environmental selection, maintaining supergene haplotypes as a balanced polymorphism. Our results provide a mechanism for the maintenance of ecotype variation in redpolls despite a genome largely homogenized by gene flow.

Variable Signatures of Selection Despite Conserved Recombination Landscapes Early in Speciation

Recently diverged taxa often exhibit heterogeneous landscapes of genomic differentiation, characterized by regions of elevated differentiation on an otherwise homogeneous background. While divergence peaks are generally interpreted as regions responsible for reproductive isolation, they can also arise due to background selection, selective sweeps unrelated to speciation, and variation in recombination and mutation rates. To investigate the association between patterns of recombination and landscapes of genomic differentiation during the early stages of speciation, we generated fine-scale recombination maps for six southern capuchino seedeaters (Sporophila) and two subspecies of White Wagtail (Motacilla alba), two recent avian radiations in which divergent selection on pigmentation genes has likely generated peaks of differentiation. We compared these recombination maps to those of Collared (Ficedula albicollis) and Pied Flycatchers (Ficedula hypoleuca), non-sister taxa characterized by moderate genomic divergence and a heterogenous landscape of genomic differentiation shaped in part by background selection. Although recombination landscapes were conserved within all three systems, we documented a weaker negative correlation between recombination rate and genomic differentiation in the recent radiations. All divergence peaks between capuchinos, wagtails, and flycatchers were located in regions with lower-than-average recombination rates, and most divergence peaks in capuchinos and flycatchers fell in regions of exceptionally reduced recombination. Thus, co-adapted allelic combinations in these regions may have been protected early in divergence, facilitating rapid diversification. Despite largely conserved recombination landscapes, divergence peaks are specific to each focal comparison in capuchinos, suggesting that regions of elevated differentiation have not been generated by variation in recombination rate alone.

The genetic basis of spatial cognitive variation in a food-caching bird

Spatial cognition is used by most organisms to navigate their environment. Some species rely particularly heavily on specialized spatial cognition to survive, suggesting that a heritable component of cognition may be under natural selection. This idea remains largely untested outside of humans, perhaps because cognition in general is known to be strongly affected by learning and experience.^1-4 We investigated the genetic basis of individual variation in spatial cognition used by non-migratory food-caching birds to recover food stores and survive harsh montane winters. Comparing the genomes of wild, free-living birds ranging from best to worst in their performance on a spatial cognitive task revealed significant associations with genes involved in neuron growth and development and hippocampal function. These results identify candidate genes associated with differences in spatial cognition and provide a critical link connecting individual variation in spatial cognition with natural selection.

Estimating hybridization in the wild using citizen science data: a path forward

Genomic evidence of introgression in natural populations has reinvigorated the study of hybridization in recent years. Still, it is largely unknown how frequently individual organisms mate across species lines. Recently, Justyn et al. 2020 suggested that eBird, one of the world's largest citizen science databases, may supply adequate data for estimating hybridization rates. Here, we compare Justyn et al.'s estimates-and their conclusions that hybridization is rare-with estimates from museum and molecular data. We also estimate hybridization using eBird observations from areas and times when hybridization is possible, namely, in contact zones during the breeding season. These estimates are all considerably higher than those reported in Justyn et al., emphasizing that inferences from multiple datasets can differ radically. Finally, we demonstrate an approach for predicting the location of hybrid zones using eBird data, which can be done with high confidence and with unprecedented resolution. We show that citizen science data, far from settling the question of how frequently bird species hybridize, instead offer a promising step toward more focused study of hybrid zones. This article is protected by copyright. All rights reserved.

A highly invasive malaria parasite has expanded its range to non-migratory birds in North America

Parasite range expansions are a direct consequence of globalization and are an increasing threat to biodiversity. Here, we report a recent range expansion of the SGS1 strain of a highly invasive parasite, Plasmodium relictum, to two non-migratory passerines in North America. Plasmodium relictum is considered one of the world's most invasive parasites and causes the disease avian malaria: this is the first reported case of SGS1 in wild non-migratory birds on the continent. Using a long-term database where researchers report avian malaria parasite infections, we summarized our current understanding of the geographical range of SGS1 and its known hosts. We also identified the most likely geographical region of this introduction event using the MSP1 allele. We hypothesize that this introduction resulted from movements of captive birds and subsequent spillover to native bird populations, via the presence of competent vectors and ecological fitting. Further work should be conducted to determine the extent to which SGS1 has spread following its introduction in North America.

Extensive historical and contemporary hybridization suggests premating isolation in Vermivora warblers is not strong: A reply to Confer et al

We present comments on an article published by Confer et al. (Ecology and Evolution, 10, 2020). Confer et al. (2020) aggregate data from multiple studies of social pairing between Vermivora chrysoptera and V. cyanoptera, two wood warblers in the family Parulidae that hybridize extensively where they co‐occur. From analysis of these data, they conclude there is near‐complete reproductive isolation between these two species. In our reply, we show that this finding is not supported by other lines of evidence, and significant drawbacks of their study design preclude such strong conclusions. In our critique, we show that (a) coarse‐scale plumage classifications cannot be used to accurately estimate hybrid ancestry in Vermivora; (b) extra‐pair paternity is very high in Vermivora and is likely facilitating hybridization, yet was not considered by Confer et al. (2020), and we suggest this will have a substantial influence on the interpretation of reproductive isolation in the system; and (c) the central finding of strong total reproductive isolation is not compatible with the results of other long‐term studies, which demonstrate low isolation and high gene flow. We conclude with a more comprehensive interpretation of hybridization and reproductive isolation in Vermivora warblers.

Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater

Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.

A122 WATER EXCHANGE FACILITATES HIGH CECAL INTUBATION RATE FOLLOWING INCOMPLETE COLONOSCOPY

Background

Incomplete colonoscopy is a complex problem that negatively affects the success of colon cancer screening programs. Failure to intubate the cecum is associated with a significant risk of missed colorectal cancer and increases costs through missed diagnoses and salvage investigations. Water exchange (WE) colonoscopy is associated with a high rate of patient comfort and cecal intubation (CI) and may be of value in preventing and following up on incomplete colonoscopy.

Aims

To estimate effectiveness of WE colonoscopy as initial salvage of incomplete colonoscopy.

Methods

All patients referred to the Kelowna Gastroenterology group for incomplete colonoscopy between Jan 2010 to Dec 2019 were included. Demographic, clinical, procedural, and pathological information were collected via retrospective chart review. Patients underwent WE colonoscopy by a single endoscopist. The outcomes evaluated were CI rate, sedation requirements, and adenoma detection.

Results

116 patients met study criteria and underwent WE colonoscopy after a previously failed or incomplete colonoscopy for technical reasons. The mean age was 66 years (range 21–89). 83 (72%) patients were female. 53 (46%) patients had previous abdominal surgery, and 42 (36%) had previous pelvic surgery. 65 (56%) patients had previous bowel disease. 81 (70%) patients had previously incomplete conventional air insufflation (AI) colonoscopy, 9 (8%) patients had previously incomplete WE colonoscopy, and 5 (4%) patients underwent unsuccessful combination of WE and AI colonoscopy. 17 (15%) patients had previously incomplete flexible sigmoidoscopy, and 4 (3%) patients had previously incomplete water immersion colonoscopy. The most common cause of unsuccessful CI was redundant colon (n=39, 34%) followed by strictures/angulations (n=16, 14%). 105 (91%) patients underwent repeat WE colonoscopy only, while 7 (6%) patients had combination WE and AI colonoscopy and 4 (3%) patients had concurrent gastroscopy. CI was successful in 114 (98%) patients and unsuccessful in 2 (2%) patients. 87 (75%) study patients received conscious sedation, 16 (14%) opted for no sedation, and 7 (6%) attempted no sedation then switched to conscious sedation. 5 patients (4%) required general anesthesia. CI was achieved in all 16 unsedated patients. 236 polyps were identified in 79 (68%) patients, 2 (1%) of which were malignant.

Conclusions

There is no standardized approach to incomplete colonoscopy. In this cohort of patients with previous failed attempt at colonoscopy, WE as a primary technique was associated with a high success rate with minimal need for general anesthesia and a high rate of polyp detection. A significant rate of colon cancer was identified, similar to that seen in general screening populations.

Funding Agencies

None

An isolated white-tailed deer (Odocoileus virginianus) population on St. John, US Virgin Islands shows low inbreeding and comparable heterozygosity to other larger populations

This is the first study to document the genetic diversity of the white-tailed deer population on St. John, US Virgin Islands. The island population was founded by a small number of animals, has very limited hunting or predation, and recently experienced a reduction in size following an extended drought in 2015. DNA samples were collected from hair from 23 anesthetized adult deer (13 males, 10 females) ranging in age from 1 to 8 years (3.36 ± 1.9 years) and also from fecal DNA samples, for a total of 42 individuals analyzed for genetic diversity. The St. John deer data set averaged 4.19 alleles per marker and demonstrates the second lowest number of alleles (A) when compared to other populations of Odocoileus virginianus (4.19). Heterozygosity was similar to the other studies (0.54) with little evidence of inbreeding. To explain the level of heterozygosity and level of inbreeding within the St. John population, three hypotheses are proposed, including the effect of intrinsic biological traits within the population, a recent infusion of highly heterogeneous loci from North American populations, and a consistent level of immigration from a nearby island. Additional work is needed to further understand the genetic history of the St. John and regional deer populations.

Asymmetric introgression reveals the genetic architecture of a plumage trait

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

Hybrid zones are windows into the evolutionary process. Semenov et al. find that the head plumage differences between white wagtail subspecies have a simple genetic basis involving two small genetic regions, in which partially dominant and epistatic interactions help to explain how this sexual signal has become decoupled from other plumage traits.

Opportunities in cancer imaging: a review of oesophageal, gastric and colorectal malignancies

The incidence of gastrointestinal (GI) malignancy is increasing worldwide. In particular, there is a concerning rise in incidence of GI cancer in younger adults. Direct endoscopic visualisation of luminal tumour sites requires invasive procedures, which are associated with certain risks, but remain necessary because of limitations in current imaging techniques and the continuing need to obtain tissue for diagnosis and genetic analysis; however, management of GI cancer is increasingly reliant on non-invasive, radiological imaging to diagnose, stage, and treat these malignancies. Oesophageal, gastric, and colorectal malignancies require specialist investigation and treatment due to the complex nature of the anatomy, biology, and subsequent treatment strategies. As cancer imaging techniques develop, many opportunities to improve tumour detection, diagnostic accuracy and treatment monitoring present themselves. This review article aims to report current imaging practice, advances in various radiological modalities in relation to GI luminal tumour sites and describes opportunities for GI radiologists to improve patient outcomes.

Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist

Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.].

Leveraging eDNA to expand the study of hybrid zones

Hybrid zones are important windows into ecological and evolutionary processes. Our understanding of the significance and prevalence of hybridization in nature has expanded with the generation and analysis of genome‐spanning data sets. That said, most hybridization research still has restricted temporal and spatial resolution, which limits our ability to draw broad conclusions about evolutionary and conservation related outcomes. Here, we argue that rapidly advancing environmental DNA (eDNA) methodology could be adopted for studies of hybrid zones to increase temporal sampling (contemporary and historical), refine and geographically expand sampling density, and collect data for taxa that are difficult to directly sample. Genomic data in the environment offer the potential for near real‐time biological tracking of hybrid zones, and eDNA provides broad, but as yet untapped, potential to address eco‐evolutionary questions.

Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone

The study of hybrid zones can provide insight into the genetic basis of species differences that are relevant for the maintenance of reproductive isolation. Hybrid zones can also provide insight into climate change, species distributions, and evolution. The hybrid zone between black-capped chickadees (Poecile atricapillus) and Carolina chickadees (Poecile carolinensis) is shifting northward in response to increasing winter temperatures but is not increasing in width. This pattern indicates strong selection against chickadees with admixed genomes. Using high-resolution genomic data, we identified regions of the genomes that are outliers in both time points and do not introgress between the species; these regions may be involved in the maintenance of reproductive isolation. Genes involved in metabolic regulation processes were overrepresented in this dataset. Several gene ontology categories were also temporally consistent-including glutamate signaling, synaptic transmission, and catabolic processes-but the nucleotide variants leading to this pattern were not. Our results support recent findings that hybrids between black-capped and Carolina chickadees have higher basal metabolic rates than either parental species and suffer spatial memory and problem-solving deficits. Metabolic breakdown, as well as spatial memory and problem-solving, in hybrid chickadees may act as strong postzygotic isolation mechanisms in this moving hybrid zone.

A273 ENDOSCOPIC RETROGRADE CHOLANGIOPANCREATOGRAPHY IN A TERTIARY CANADIAN HOSPITAL: OPTIMIZING TISSUE SAMPLING TECHNIQUES

Background

Pancreatic and biliary cancer can be difficult to definitively diagnose, and tissue diagnosis defines clinical management in both early and late disease. The majority of patients with pancreaticobiliary malignancy present with late disease and only 30% have resectable tumours, contributing to poor prognosis and outcome. Endoscopic retrograde cholangiopancreatography (ERCP) is a mainstay for diagnosing and treating conditions of the bile and pancreatic duct.

Aims

This study aimed to provide data on the diagnostic performance of ERCP utilizing conventional methods for tissue acquisition particularly in the setting of an indeterminate stricture. In particular, this was a quality assurance review to determine our centre’s baseline performance as a reference so new methods of tissue acquisition such as SpyglassTM can be benchmarked against.

Methods

In a tertiary care hospital, 3723 ERCP procedures were performed between 2013 and 2017. Demographic and clinical information was retrospectively collected. Demographic and clinical information was collected. Three ERCP techniques of tissue sampling were analyzed: brushing alone (BiA), biopsy alone (BrA), and brushing and biopsy dual-modality approach (BrBi). The diagnostic performances (sensitivity, specificity, and accuracy) were calculated with data from post-sampling clinical reports, surgical pathological reports, and diagnostic imaging reports.

Results

222 patients (285 ERCP procedure) met the study criteria and received fluoroscopy-guided ERCP sampling with cytology brushing and/or tissue biopsies. 36 (13%) patients had BiA, 85 (29%) patients had BrA, and 164 (58%) patients had BrBi. The sensitivities, specificities, and accuracies of the three sampling techniques respectively were: 56%, 93%, and 85% for BiA; 73%, 96%, and 83% for BrA; and 79%, 94%, and 86% for BrBi.

Conclusions

Our retrospective analysis of fluoroscopic-guided tissue acquisition shows accuracy as high as current published data on direct visualization cholangiosopy guided techniques. A prospective study looking not only at clinical yield but a cost analysis should be put in place prior to a commitment to purchase new equipment such as the SpyglassTM.

Funding Agencies

None

Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird

Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.

A wood-warbler produced through both interspecific and intergeneric hybridization

Hybridization between divergent taxa can provide insight into the breakdown of characters used in mate choice, as well as reproductive compatibility across deep evolutionary timescales. Hybridization can also occur more frequently in declining populations, as there is a smaller pool of conspecific mates from which to choose. Here, we report an unusual combination of factors that has resulted in a rare, three-species hybridization event among two genera of warblers, one of which is experiencing significant population declines. We use bioacoustic, morphometric and genetic data, to demonstrate that an early generation female hybrid between a golden-winged warbler (Vermivora chrysoptera) and a blue-winged warbler (V. cyanoptera) went on to mate and successfully reproduce with a chestnut-sided warbler (Setophaga pensylvanica). We studied the product of this event-a putative chrysoptera × cyanoptera × pensylvanica hybrid-and show that this male offspring sang songs like S. pensylvanica, but had morphometric traits similar to Vermivora warblers. The hybrid's maternal parent had V. chrysoptera mitochondrial DNA and, with six plumage-associated loci, we predicted the maternal parent's phenotype to show that it was likely an early generation Vermivora hybrid. That this hybridization event occurred within a population of Vermivora warblers in significant decline suggests that females may be making the best of a bad situation, and that wood-warblers in general have remained genetically compatible long after they evolved major phenotypic differences.

The evolution of magnetic resonance enterography in the assessment of motility disorders in children

Gastrointestinal symptoms including constipation, diarrhoea, pain and bloating represent some of the most common clinical problems for patients. These symptoms can often be managed with cheap, widely available medication or will spontaneously resolve. However, for many patients, chronic GI symptoms persist and frequently come to dominate their lives. At one end of the spectrum there is Inflammatory Bowel Disease (IBD) with a clearly defined but expensive treatment pathway. Contrasting with this is Irritable Bowel Syndrome (IBS), likely a collection of pathologies, has a poorly standardised pathway with unsatisfactory clinical outcomes. Managing GI symptoms in adult populations is a challenge. The clinical burden of gastrointestinal disease is also prevalent in paediatric populations and perhaps even harder to treat. In this review we explore some of the recent advances in magnetic resonance imaging (MRI) to study the gastrointestinal tract. Complex in both its anatomical structure and its physiology we are likely missing key physiological markers of disease through relying on symptomatic descriptors of gut function. Using MRI we might be able to characterise previously opaque processes, such as non-propulsive contractility, that could lead to changes in how we understand even common symptoms like constipation. This review explores recent advances in the field in adult populations and examines how this safe, objective and increasingly available modality might be applied to paediatric populations.

MRI assessment of the postprandial gastrointestinal motility and peptide response in healthy humans

BACKGROUND

Feeding triggers inter-related gastrointestinal (GI) motor, peptide and appetite responses. These are rarely studied together due to methodological limitations. Recent MRI advances allow pan-intestinal, non-invasive assessment of motility in the undisturbed gut. This study aimed to develop a methodology to assess pan-intestinal motility and transit in a single session using MRI and compare imaging findings to GI peptide responses to a test meal and symptoms in a healthy volunteer cohort.

METHODS

Fifteen healthy volunteers (29.3±2.7 years and BMI 20.1±1.2 kg m^-2 ) underwent baseline and postprandial MRI scans, symptom questionnaires, and blood sampling (for subsequent GI peptide analysis, Glucagon-like peptide-1 [GLP-1], Polypeptide YY [PYY], Cholecystokinin [CCK]) at intervals for 270 minutes following a 400 g soup meal (204 kcal, Heinz, UK). Gastric volume, gall bladder volume, small bowel water content, small bowel motility, and whole gut transit were measured from the MRI scans.

KEY RESULTS

(mean±SEM) Small bowel motility index increased from fasting 39±3 arbitrary units (a.u.) to a maximum of 87±7 a.u. immediately after feeding. PYY increased from fasting 98±10 pg mL^-1 to 149±14 pg mL^-1 at 30 minutes and GLP-1 from fasting 15±3 μg mL^-1 to 22±4 μg mL^-1 . CCK increased from fasting 0.40±0.06 pmol mL^-1 to 0.94±0.1 pmol mL^-1 . Gastric volumes declined with a T_1/2 of 46±5 minute and the gallbladder contracted from a fasting volume of 19±2 mL^-1 to 12±2 mL^-1 . Small bowel water content increased from 39±2 mL^-1 to 51±2 mL^-1 postprandial. Fullness VAS score increased from 9±5 mm to 41±6 mm at 30 minutes postprandial.

CONCLUSIONS AND INFERENCES

The test meal challenge was effective in inducing a change in MRI motility end-points which will improve understanding of the pathophysiological postprandial GI response.

The development of a magnetic resonance imaging index for fistulising Crohn's disease

BACKGROUND

Magnetic resonance imaging (MRI) is the gold standard for assessment of perianal fistulising Crohn's disease (CD). The Van Assche index is the most commonly used MRI fistula index.

AIMS

To assess the reliability of the Van Assche index, and to modify the instrument to improve reliability and create a novel index for fistulising CD.

METHODS

A consensus process developed scoring conventions for existing Van Assche index component items and new items. Four experienced radiologists evaluated 50 MRI images in random order on three occasions. Reliability was assessed by estimates of intraclass correlation coefficients (ICCs). Common sources of disagreement were identified and recommendations made to minimise disagreement. A mixed effects model used a 100 mm visual anologue scale (VAS) for global severity as outcome and component items as predictors to create a modified Van Assche index.

RESULTS

Intraclass correlation coefficients (95% confidence intervals) for intra-rater reliability of the original and modified Van Assche indices and the VAS were 0.86 (0.81-0.90), 0.90 (0.86-0.93) and 0.86 (0.82-0.89). Corresponding ICCs for inter-rater reliability were 0.66 (0.52-0.76), 0.67 (0.55-0.75) and 0.58 (0.47-0.66). Sources of disagreement included number, location, and extension of fistula tracts, and rectal wall involvement. A modified Van Assche index (range 0-24) was created that included seven component items.

CONCLUSIONS

Although "almost perfect" intra-rater reliability was observed for the assessment of MRI images for fistulising CD using the Van Assche index, inter-rater reliability was considerably lower. Our modification of this index should result in a more optimal instrument.

A magnetic resonance imaging study of gastric motor function in patients with dyspepsia associated with Ehlers-Danlos Syndrome-Hypermobility Type: A feasibility study

BACKGROUND

The clinical use of Magnetic Resonance Imaging (MRI) for investigating gastric motor function in dyspepsia is limited, largely due to protocol complexity, cost and limited availability. In this study, we explore the feasibility of a sub 60-minute protocol using a water challenge to assess gastric emptying, motility and accommodation in a cohort of Ehlers-Danlos Syndrome-Hypermobility type (EDS-HT) patients presenting with dyspepsia.

METHODS

Nine EDS-HT patients (mean age 33, range: 26-50 all female) with a history of dyspepsia were recruited together with nine-matched controls. Subjects fasted for 6 hours prior to MRI. A baseline anatomical and motility scan was performed after which the subjects ingested 300 mL water. The anatomical and motility scans were then repeated every 10 minutes to a total of 60 minutes. Gastric emptying time, motility, and accommodation were calculated based on the observations of two observers for each EDS-HT subject and compared to their matched control using paired statistics.

KEY RESULTS

Median motility increase following the water challenge was lower in EDS-HT subjects (11%, range: 0%-22%) compared to controls (22%, range: 13%-56%), P=.03. Median gastric emptying time was non-significantly decreased in EDS-HT subjects (12.5 minutes, range: 6-27) compared to controls (20 minutes, range: 7-30), P=.15. Accommodation was non-significantly reduced in EDS-HT subjects (56% increase, range: 32%-78%) compared to healthy controls (67% increase, range: 52%-78%), P=.19.

CONCLUSIONS & INFERENCES

This study demonstrates the feasibility of a water challenge MRI protocol to evaluate gastric physiology in the clinical setting. Motility differences between EDS-HT and controls are worthy of further investigation.

Safety and acceptability of an organic light-emitting diode sleep mask as a potential therapy for retinal disease

PurposeThe purpose of the study was to study the effect of an organic light-emitting diode sleep mask on daytime alertness, wellbeing, and retinal structure/function in healthy volunteers and in diabetic macular oedema (DMO).Patients and methodsHealthy volunteers in two groups, 18-30 yrs (A), 50-70 yrs (B) and people with DMO (C) wore masks (504 nm wavelength; 80 cd/m² luminance; ≤8 h) nightly for 3 months followed by a 1-month recovery period. Changes from baseline were measured for (means): psychomotor vigilance task (PVT) (number of lapses (NL), response time (RT)), sleep, depression, psychological wellbeing (PW), visual acuity, contrast sensitivity, colour, electrophysiology, microperimetry, and retinal thickness on OCT.ResultsOf 60 participants, 16 (27%) withdrew, 8 (13%) before month 1, due to sleep disturbances and mask intolerance. About 36/55 (65%) who continued beyond month 1 reported ≥1 adverse event. At month 3 mean PVT worsened in Group A (RT (7.65%, P<0.001), NL (43.3%, P=0.005)) and mean PW worsened in all groups (A 28.0%, P=0.01, B 21.2%, P=0.03, C 12.8%, P<0.05). No other clinically significant safety signal was detected. Cysts reduced/resolved in the OCT subfield of maximal pathology in 67% Group C eyes. Thinning was greater at 3 and 4 months for greater baseline thickness (central subfield P<0.001, maximal P<0.05).ConclusionSleep masks showed no major safety signal apart from a small impairment of daytime alertness and a moderate effect on wellbeing. Masks were acceptable apart from in some healthy participants. Preliminary data suggest a beneficial effect on retinal thickness in DMO. This novel therapeutic approach is ready for large clinical trials.

Foliar nectar enhances plant-mite mutualisms: the effect of leaf sugar on the control of powdery mildew by domatia-inhabiting mites

BACKGROUND AND AIMS

Mite domatia are small structures on the underside of plant leaves that provide homes for predacious or fungivorous mites. In turn, mites inhabiting domatia defend the plant by consuming leaf herbivores and pathogens, which can result in a domatia-mediated, plant-mite defence mutualism. Several recent studies have suggested that plants receive enhanced benefits when they provide a foliar food source, such as sugars secreted from extrafloral nectaries, to mite mutualists alongside mite domatia. However, the effect of foliar sugar on reducing leaf pathogen load via domatia-inhabiting mites has not been directly investigated.

METHODS

To fill this gap, the links between foliar sugar addition, domatia-inhabiting mite abundance, and pathogen load were experimentally evaluated in wild grape. Furthermore, because the proposed combined benefits of providing food and housing have been hypothesized to select for the evolutionary correlation of extrafloral nectaries and domatia across plant lineages, a literature survey aimed at determining the overlap of mite domatia and extrafloral nectaries across plant groups was also conducted.

KEY RESULTS

It was found that leaves with artificial addition of foliar sugar had 58-80 % more mites than leaves without foliar sugar addition, and that higher mite abundances translated to reduced powdery mildew (Erysiphe necator) loads on leaves. It was found that mite domatia and extrafloral nectaries occur non-randomly in the same clades across Eudicots. Genera with both traits are reported to highlight candidate lineages for future studies.

CONCLUSIONS

Together, the results demonstrate that foliar sugar can indeed enhance the efficacy of domatia-mediated plant-mite mutualisms, and suggest that this synergism has the potential to influence the co-distribution of foliar nectar and mite domatia across plants.