Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant-calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate to what extent the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find greatest topological accuracy when filtering sites for minor allele count >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with minor allele count >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short read genomic data for phylogenetic inference.

The smelly path to sympatric speciation?

In this issue of Molecular Ecology, Poelstra et al. () use genomic data to show that cichlid species in the adaptive radiation in Lake Ejagham, Cameroon, experienced gene flow with a riverine relative, primarily prior to their diversification. Intriguingly, this introgression brought with it olfactory alleles that the authors suggest may play a sensory role in speciation. As a classic example of sympatric speciation due to the highly restricted geography of this small (0.49 km² ) crater lake (Schliewen et al., ), this result sheds new light on the history of this fascinating radiation. As genomic data for cichlid radiations accumulate, finding evidence of introgression increasingly appears to be the rule rather than the exception (Kautt et al., ; Meier et al., , ). However, two points are pressing as evidence for introgression mounts: (a) It is crucial to understand the assumptions of analytical approaches used and (b) it is important to think clearly about the divergent contexts in which evidence for introgression has been invoked as an important feature of adaptive radiation.

Opsin expression predicts male nuptial color in threespine stickleback

Theoretical models of sexual selection suggest that male courtship signals can evolve through the build-up of genetic correlations between the male signal and female preference. When preference is mediated via increased sensitivity of the signal characteristics, correlations between male signal and perception/sensitivity are expected. When signal expression is limited to males, we would expect to find signal-sensitivity correlations in males. Here, we document such a correlation within a breeding population of threespine stickleback mediated by differences in opsin expression. Males with redder nuptial coloration express more long-wavelength-sensitive (LWS) opsin, making them more sensitive to orange and red. This correlation is not an artifact of shared tuning to the optical microhabitat. Such correlations are an essential feature of many models of sexual selection, and our results highlight the potential importance of opsin expression variation as a substrate for signal-preference evolution. Finally, these results suggest a potential sensory mechanism that could drive negative frequency-dependent selection via male-male competition and thus maintain variation in male nuptial color.

Intruder colour and light environment jointly determine how nesting male stickleback respond to simulated territorial intrusions

Variation in male nuptial colour signals might be maintained by negative frequency-dependent selection. This can occur if males are more aggressive towards rivals with locally common colour phenotypes. To test this hypothesis, we introduced red or melanic three-dimensional printed-model males into the territories of nesting male stickleback from two optically distinct lakes with different coloured residents. Red-throated models were attacked more in the population with red males, while melanic models were attacked more in the melanic male lake. Aggression against red versus melanic models also varied across a depth gradient within each lake, implying that the local light environment also modulated the strength of negative frequency dependence acting on male nuptial colour.

Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?

Background

Major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. However one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. We applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of Labridae and within the subclade of parrotfishes.

Results

Diversification patterns within early labrids did not reflect rapid initial radiation. Much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. A secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. However diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications.

Conclusion

The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within Scarus and Chlorurus. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. We suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification.

DO REEFS DRIVE DIVERSIFICATION IN MARINE TELEOSTS? EVIDENCE FROM THE PUFFERFISH AND THEIR ALLIES (ORDER TETRAODONTIFORMES)

A major challenge in evolutionary biology lies in explaining patterns of high species numbers found in biodiversity hot spots. Tropical coral reefs underlie most marine hot spots and reef-associated fish faunas represent some of the most diverse assemblages of vertebrates on the planet. Although the standing diversity of modern reef fish clades is usually attributed to their ecological association with corals, untangling temporal patterns of codiversification has traditionally proved difficult. In addition, owing to uncertainty in higher-level relationships among acanthomorph fish, there have been few opportunities to test the assumption that reef-association itself leads to higher rates of diversification compared to other habitats. Here we use relaxed-clock methods in conjunction with statistical measures of species accumulation and phylogenetic comparative methods to clarify the temporal pattern of diversification in reef and nonreef-associated lineages of tetraodontiforms, a morphologically diverse order of teleost fish. We incorporate 11 fossil calibrations distributed across the tetraodontiform tree to infer divergence times and compare results from models of autocorrelated and uncorrelated evolutionary rates. All major tetraodontiform reef crown groups have significantly higher rates of diversification than the order as a whole. None of the nonreef-associated families show this pattern with the exception of the aracanid boxfish. Independent contrasts analysis also reveals a significantly positive relationship between diversification rate and proportion of reef-associated species within each family when aracanids are excluded. Reef association appears to have increased diversification rate within tetraodontiforms. We suggest that both intrinsic factors of reef habitat and extrinsic factors relating to the provincialization and regionalization of the marine biota during the Miocene (about 23-5 MY) played a role in shaping these patterns of diversity.

Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia

Bacterial endosymbionts are widespread across several insect orders and are involved in interactions ranging from obligate mutualism to reproductive parasitism. Candidatus Blochmannia gen. nov. (Blochmannia) is an obligate bacterial associate of Camponotus and related ant genera (Hymenoptera: Formicidae). The occurrence of Blochmannia in all Camponotus species sampled from field populations and its maternal transmission to host offspring suggest that this bacterium is engaged in a long-term, stable association with its ant hosts. However, evidence for cospeciation in this system is equivocal because previous phylogenetic studies were based on limited gene sampling, lacked statistical analysis of congruence, and have even suggested host switching. We compared phylogenies of host genes (the nuclear EF-1alphaF2 and mitochondrial COI/II) and Blochmannia genes (16S ribosomal DNA [rDNA], groEL, gidA, and rpsB), totaling more than 7 kilobases for each of 16 Camponotus species. Each data set was analyzed using maximum likelihood and Bayesian phylogenetic reconstruction methods. We found minimal conflict among host and symbiont phylogenies, and the few areas of discordance occurred at deep nodes that were poorly supported by individual data sets. Concatenated protein-coding genes produced a very well-resolved tree that, based on the Shimodaira-Hasegawa test, did not conflict with any host or symbiont data set. Correlated rates of synonymous substitution (d(S)) along corresponding branches of host and symbiont phylogenies further supported the hypothesis of cospeciation. These findings indicate that Blochmannia-Camponotus symbiosis has been evolutionarily stable throughout tens of millions of years. Based on inferred divergence times among the ant hosts, we estimated rates of sequence evolution of Blochmannia to be approximately 0.0024 substitutions per site per million years (s/s/MY) for the 16S rDNA gene and approximately 0.1094 s/s/MY at synonymous positions of the genes sampled. These rates are several-fold higher than those for related bacteria Buchnera aphidicola and Escherichia coli. Phylogenetic congruence among Blochmannia genes indicates genome stability that typifies primary endosymbionts of insects.

The current status of Balint groups in US family practice residencies: A 10-year follow-up study, 1990-2000

BACKGROUND AND OBJECTIVES

In 1990, the first and, to date, only objective study of Balint groups in US family practice residencies was conducted to measure their prevalence, composition, leadership, and function. The study reported here collected similar information about Balint groups.

METHODS

Surveys were sent to all 464 US family practice residency program directors, with a 1-month follow-up to nonrespondents. The survey included questions about the existence, leadership, meeting frequency, and objectives of Balint training.

RESULTS

A total of 298 (64%) residencies responded. Almost half (48%) of US responding residences reported conducting Balint groups, and 40% of those residencies have more than one group. The frequency of Balint group meetings has shifted in the past 10 years. In 1990, 55% of groups met weekly; in 2000, only 15% of groups met weekly. Sixty-five percent of residencies require Balint participation. One third of Balint groups are conducted without a coleader and the number of physicians leading groups is 22%, a decrease of 10% from 10 years ago. Forty-four percent of groups are led by psychologists, an increase of 19% from 10 years ago. Respondents indicated uncertainly about whether their groups were true Balint groups or simply resident support groups.

CONCLUSIONS

About half of US family practice residencies operate groups described as Balint groups. They meet less frequently then 10 years ago and are less likely to have a physician involved in group leadership. Some of the groups may actually be support groups rather than Balint groups.

Approach to bloody stools in adults

The mortality from LIB is less than 5%. The bleeding in the majority of patients with LIB resolves spontaneously and usually leaves no lasting sequelae. Early colonoscopy may shorten the length and cost of hospitalization.

Balint group observations: the white knight and other heroic physician roles

BACKGROUND

This article reports a typology of five roles that resident family physicians on occasion assume when relating to troubling patients presented in Balint group seminars. The five roles include the white knight (my way or no way), the Pogo look-alike (I feel your pain), the missing link (you made me do it), the surrogate (I can help), and the revolutionary (let me show you). Each role reflects a particular physician's coping behavior in the context of a specific troubling relationship and is driven, in large part, by unrealistic professional expectations. The roles intend to perform a heroic function in rescuing or protecting the patient, the family, or the physician from a distressing medical situation. Balint group work provides participants with the opportunity to derive clinically useful meaning from their presentations. Residents begin to imagine a variety of therapeutic (helpful) roles to replace the ones they were induced to fill. This process has implications for practicing physicians and physician teachers for improving patient and doctor satisfaction and well-being.

Comorbidity of posttraumatic stress disorder and irritable bowel syndrome

BACKGROUND

Irritable bowel syndrome (IBS) is a chronic disorder that has been found to be associated with psychiatric disorders and a history of physical and/or sexual abuse. To date, the relationship of posttraumatic stress disorder (PTSD) and IBS has not been investigated. The primary purpose of this study was to examine the relationship of IBS and PTSD.

METHOD

Fifty consecutive IBS patients admitted to a clinical treatment study were assessed for IBS, trauma history, and psychiatric disorders.

RESULTS

Twenty-seven IBS patients (54%) met criteria for a psychiatric diagnosis at some time in their lives. Twenty-two patients (44%) reported a trauma history. Eighteen (36%) were diagnosed with PTSD. Those IBS patients with a trauma history were more likely to have other comorbid psychiatric diagnoses.

CONCLUSION

These results suggest that IBS is often associated with psychiatric disorders, indicating that assessment and treatment of these comorbid conditions may be important in the treatment of IBS. PTSD, which had not been previously investigated in relation to IBS, had a high prevalence, indicating the need for careful trauma and PTSD assessment in patients with IBS. Patients with IBS who have a trauma history may be more at risk for other comorbid psychiatric disorders than IBS patients without a trauma history.

Family practice residents' perspectives on Balint group training: in-depth interviews with frequent and infrequent attenders

BACKGROUND

Balint groups are focused discussion groups that help students, residents, or physicians respond empathetically to their patients and recognize underlying psychosocial elements in patients' complaints. Approximately 40% to 60% of residents who start optional Balint group training show infrequent attendance. The primary objective of this study was to interview frequent and nonfrequent attenders to assess the value of Balint group training from the residents' perspective and to explain why many residents attend Balint group meetings infrequently or discontinue Balint training altogether.

METHODS

Two methods were used to discern differences between frequent attenders and infrequent attenders: (1) evaluation of Myers-Briggs Type Indicator (MBTI) data collected at the beginning of the residency program, and (2) semi-structured personal interviews with both frequent and infrequent attenders.

RESULTS

MBTI data showed frequent attenders to have higher scores than infrequent attenders in the intuitive dimension. Interviews with Balint group attenders showed strong perception about the value of this training. The majority felt Balint training had improved their effectiveness as family physicians, specifically when dealing with troubling patients. Infrequent attenders mentioned scheduling problems and a variety of emotional/personality factors as reasons for not attending Balint seminars. Frequent attenders attributed nonattendance in others to lack of interest in the psychodynamics of the doctor-patient relationship and differences in personality type.

CONCLUSION

Residents who participated in Balint groups perceive this training as helpful in understanding themselves in relationships with their patients. However, the study results suggest that many residents choose not to attend optional Balint group seminars because of emotional or personality variables, such as anxiety about self-disclosure and introversion. While Balint groups are a valuable component of a family practice residency program, it is likely that not all residents will be motivated or capable of deriving benefits from this teaching approach.

Empathy: an essential skill for understanding the physician-patient relationship in clinical practice

In clinical practice, empathy is the skill used by physicians to decipher and respond to thoughts and feelings in the physician-patient relationship. Empathetic understanding and empathetic response occur in three phases of every office visit: the negotiation phase, the clinical reasoning phase, and the establishment of therapeutic alliance. Masters of empathetic skills is difficult, and before teaching empathy to residents and students, teachers must first develop their own empathetic skills. Development of empathetic skills can occur in Balint training programs, through the use of audio- or videotaped patient encounters, or through one-on-one training with an experienced preceptor.

Gearing balint group leadership to resident professional development

This paper discusses the sequential phases of typical Balint training groups. The cases presented reflect the presenters' professional developmental time line and serve the participants' developmental needs: exploring professional boundaries and intragroup intimacy. The activities and issues arising in the meetings stem from these developmental needs and help the group members acquire specific skills. Knowing where the group members are in their professional development should help group leaders give a seminar its focus, decide on group membership, and recognize when a group is not developing appropriately.

A survey of Balint group activities in U.S. family practice residency programs

The investigators conducted a survey of Balint group activities among family practice residencies in the United States. The survey was designed to discover how many programs have Balint groups as well as the groups' characteristics, leadership, and structure. Of the 381 family practice residencies surveyed, 93% responded. Of those, 66 offered Balint seminars to 115 different groups. Most groups met at weekly intervals for two to three years. Most groups were led by family physicians (32%), psychologists (25%), or social workers (19%). Most leaders followed the format of a spontaneous case presentation from memory. Support for residents and resolution of professional role conflict were rated as the two major objectives of training. The leaders rated an understanding of feelings generated when with patients and an enhanced sense of professional self-worth as the most attainable attitudinal changes.

Balint group leadership by a family physician in a residency program

The historical background of Balint groups is summarized. Specific details about initial recruitment of residents and establishment of guidelines for group function are discussed. The central importance of quality control to the leader is emphasized. Qualifications for a nonanalyst family physician group leader are suggested. Results of resident evaluations indicates the educational merit of such training. Balint training provides pragmatic, clinically-oriented research, which is fundamental for all family medicine residencies.