Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data.

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].

Does Context Count? The Association Between Quality of Care and Job Characteristics in Residential Aged Care and Hospital Settings: A Systematic Review and Meta-Analysis.

BACKGROUND AND OBJECTIVES: Within residential aged care settings, reduced quality of care (QoC), abuse, and neglect have been global phenomena which require urgent intervention. As the reported rate of these problems is much higher in aged care compared to hospital settings, we investigated whether differing job design characteristics between the 2 settings might explain the difference. RESEARCH DESIGN AND METHODS: We used a meta-analysis to compare differences in the relationships between high job demands, low job resources, and job strain with QoC and counterproductive work behaviors (CWBs) across aged care and hospital settings. RESULTS: Data were extracted from 42 studies (n = 55 effects). QoC was negatively correlated with high job demands (ρ¯ = -0.22, 95% confidence interval [CI]: -0.29, -0.15, k = 7), low job resources (ρ¯ = -0.40, 95% CI: -0.47, -0.32, k = 15), and job strain (ρ¯ = -0.32, 95% CI: -0.38, -0.25, k = 22), CWBs had a positive relationship with job demands (ρ¯ = 0.35, 95% CI: 0.10, 0.59, k = 3) and job strain (ρ¯ = 0.34, 95% CI: 0.13, 0.56, k = 6). The association between poor QoC and low job resources was stronger in aged care (r = -0.46, 95% CI: -0.55, -0.36, k = 8) than in hospital settings (r = -0.30, 95% CI: -0.41, -0.18, k = 7). DISCUSSION AND IMPLICATIONS: Our findings suggest that relationships between low job resources and poor QoC are exacerbated in residential aged care contexts. To improve care outcomes, stakeholders should improve job resources such as skill discretion, supervisory supports, and increased training and staffing levels in residential aged care.

Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC).

Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov Chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them.

Phylogenetic trees provide important information on the evolutionary relationships between organisms, as well as their diversification dynamics. Phylogenies are commonly built using Bayesian inference with MCMC, a powerful but also complex algorithm. This inference is implemented in software frameworks which propose a wide range of models and customization options. The amount of choices offered by these tools can be confusing for users, especially as many of these choices will affect the performance of the inference. This work is intended as a practical guide for preparing and troubleshooting a phylogenetic inference using the Bayesian MCMC method. First, we introduce the different components of this inference method, and how they are implemented in practice. We present the important factors which should be accounted for when designing a study using Bayesian phylogenetic inference with real data. We also list multiple issues which are frequently encountered by users when running the inference, and we provide advice on how to resolve these problems.

Genomic data support the taxonomic validity of Middle American livebearers Poeciliopsis gracilis and Poeciliopsis pleurospilus (Cyprinodontiformes: Poeciliidae).

Poeciliopsis (Cyprinodontiformes: Poeciliidae) is a genus comprised of 25 species of freshwater fishes. Several well-known taxonomic uncertainties exist within the genus, especially in relation to the taxonomic status of Poeciliopsis pleurospilus and P. gracilis. However, to date, no studies have been conducted to specifically address the taxonomic status of these two species. The goal of this study was to examine the taxonomic validity of P. pleurospilus and P. gracilis using genomic data (ddRADseq) in phylogenetic, population genetic, and species delimitation frameworks. Multiple analyses support the recognition of both taxa as distinct species and also permits us to revise their respective distributions. A species delimitation analysis indicates that P. pleurospilus and P. gracilis are distinct species, each of which consists of two distinct lineages that are geographically structured. Phylogenetic and population genetic analyses provide clear evidence that individuals of P. gracilis are distributed north and west of the Isthmus of Tehuantepec in both Pacific and Atlantic river systems in Mexico, whereas individuals of P. pleurospilus are distributed in both Atlantic and Pacific river systems south and east of the Isthmus of Tehuantepec, from southern Mexico to Honduras.

treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data.

The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/).

From panic to pedagogy: Using online active learning to promote inclusive instruction in ecology and evolutionary biology courses and beyond.

The rapid shift to online teaching in spring 2020 meant most of us were teaching in panic mode. As we move forward with course planning for fall and beyond, we can invest more time and energy into improving the online experience for our students. We advocate that instructors use inclusive teaching practices, specifically through active learning, in their online classes. Incorporating pedagogical practices that work to maximize active and inclusive teaching concepts will be beneficial for all students, and especially those from minoritized or underserved groups. Like many STEM fields, Ecology and Evolution shows achievement gaps and faces a leaky pipeline issue for students from groups traditionally underserved in science. Making online classes both active and inclusive will aid student learning and will also help students feel more connected to their learning, their peers, and their campus. This approach will likely help with performance, retention, and persistence of students. In this paper, we offer broadly applicable strategies and techniques that weave together active and inclusive teaching practices. We challenge instructors to commit to making small changes as a first step to more inclusive teaching in ecology and evolutionary biology courses.

Clinical and ethical challenges for emergency departments during communicable disease outbreaks: Can lessons from Ebola Virus Disease be applied to the COVID-19 pandemic?

EDs fulfil a frontline function during public health emergencies (PHEs) and will play a pivotal role during the COVID-19 pandemic. This perspective article draws on qualitative data from a longitudinal, ethnographic study of an Australian tertiary ED to illustrate the clinical and ethical challenges faced by EDs during PHEs. Interview data collected during the 2014 Ebola Virus Disease PHE of International Concern suggest that ED clinicians have a strong sense of professional responsibility, but this can be compromised by increased visibility of risk and sub-optimal engagement from hospital managers and public health authorities. The study exposes the tension between a healthcare worker's right to protection and a duty to provide treatment. Given the narrow window of opportunity to prepare for a surge of COVID-19 presentations, there is an immediate need to reflect and learn from previous experiences. To maintain the confidence of ED clinicians, and minimise the risk of moral injury, hospital and public health authorities must urgently develop processes to support ethical healthcare delivery and ensure adequate resourcing of EDs.

A Systematist's Guide to Estimating Bayesian Phylogenies From Morphological Data.

Phylogenetic trees are crucial to many aspects of taxonomic and comparative biology. Many researchers have adopted Bayesian methods to estimate their phylogenetic trees. In this family of methods, a model of morphological evolution is assumed to have generated the data observed by the researcher. These models make a variety of assumptions about the evolution of morphological characters, and these assumptions are translated into mathematics as parameters. The incorporation of prior distributions further allows researchers to quantify their prior beliefs about the value any one parameter can take. How to translate biological knowledge into mathematical language is difficult, and can be confusing to many biologists. This review aims to help systematics researchers understand the biological meaning of common models and assumptions. Using examples from the insect fossil record, I will demonstrate empirically what assumptions mean in concrete terms, and discuss how researchers can use and understand Bayesian methods for phylogenetic estimation.

Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation.

Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards-Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a radiation of salamanders (Eurycea) endemic to the Edwards-Trinity system using phylogenetic and population genetic analysis of genome-wide DNA sequence data. Results revealed complex patterns of isolation and reconnection driven by surface and subsurface hydrology, resulting in both adaptive and nonadaptive population divergence and speciation. Our results uncover cryptic species diversity and refine the borders of several threatened and endangered species. The US Endangered Species Act has been used to bring state regulation to unrestricted groundwater withdrawals in the Edwards (Balcones Fault Zone) Aquifer, where listed species are found. However, the Trinity and Edwards-Trinity (Plateau) aquifers harbor additional species with similarly small ranges that currently receive no protection from regulatory programs designed to prevent groundwater depletion. Based on regional climate models that predict increased air temperature, together with hydrologic models that project decreased springflow, we conclude that Edwards-Trinity salamanders and other codistributed groundwater-dependent organisms are highly vulnerable to extinction within the next century.

The why, when, and how of computing in biology classrooms.

Many biologists are interested in teaching computing skills or using computing in the classroom, despite not being formally trained in these skills themselves. Thus biologists may find themselves researching how to teach these skills, and therefore many individuals are individually attempting to discover resources and methods to do so. Recent years have seen an expansion of new technologies to assist in delivering course content interactively. Educational research provides insights into how learners absorb and process information during interactive learning. In this review, we discuss the value of teaching foundational computing skills to biologists, and strategies and tools to do so. Additionally, we review the literature on teaching practices to support the development of these skills. We pay special attention to meeting the needs of diverse learners, and consider how different ways of delivering course content can be leveraged to provide a more inclusive classroom experience. Our goal is to enable biologists to teach computational skills and use computing in the classroom successfully.

Phylogenetic patterns of ant-fungus associations indicate that farming strategies, not only a superior fungal cultivar, explain the ecological success of leafcutter ants.

To elucidate fungicultural specializations contributing to ecological dominance of leafcutter ants, we estimate the phylogeny of fungi cultivated by fungus-growing (attine) ants, including fungal cultivars from (i) the entire leafcutter range from southern South America to southern North America, (ii) all higher-attine ant lineages (leafcutting genera Atta, Acromyrmex; nonleafcutting genera Trachymyrmex, Sericomyrmex) and (iii) all lower-attine lineages. Higher-attine fungi form two clades, Clade-A fungi (Leucocoprinus gongylophorus, formerly Attamyces) previously thought to be cultivated only by leafcutter ants, and a sister clade, Clade-B fungi, previously thought to be cultivated only by Trachymyrmex and Sericomyrmex ants. Contradicting this traditional view, we find that (i) leafcutter ants are not specialized to cultivate only Clade-A fungi because some leafcutter species ranging across South America cultivate Clade-B fungi; (ii) Trachymyrmex ants are not specialized to cultivate only Clade-B fungi because some Trachymyrmex species cultivate Clade-A fungi and other Trachymyrmex species cultivate fungi known so far only from lower-attine ants; (iii) in some locations, single higher-attine ant species or closely related cryptic species cultivate both Clade-A and Clade-B fungi; and (iv) ant-fungus co-evolution among higher-attine mutualisms is therefore less specialized than previously thought. Sympatric leafcutter ants can be ecologically dominant when cultivating either Clade-A or Clade-B fungi, sustaining with either cultivar-type huge nests that command large foraging territories; conversely, sympatric Trachymyrmex ants cultivating either Clade-A or Clade-B fungi can be locally abundant without achieving the ecological dominance of leafcutter ants. Ecological dominance of leafcutter ants therefore does not depend primarily on specialized fungiculture of L. gongylophorus (Clade-A), but must derive from ant-fungus synergisms and unique ant adaptations.

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

Inferring node dates from tip dates in fossil Canidae: the importance of tree priors.

Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.

Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors.

The Mk model was developed for estimating phylogenetic trees from discrete morphological data, whether for living or fossil taxa. Like any model, the Mk model makes a number of assumptions. One assumption is that transitions between character states are symmetric (i.e., the probability of changing from 0 to 1 is the same as 1 to 0). However, some characters in a data matrix may not satisfy this assumption. Here, we test methods for relaxing this assumption in a Bayesian context. Using empirical data sets, we perform model fitting to illustrate cases in which modeling asymmetric transition rates among characters is preferable to the standard Mk model. We use simulated data sets to demonstrate that choosing the best-fit model of transition-state symmetry can improve model fit and phylogenetic estimation.

Shared Escovopsis parasites between leaf-cutting and non-leaf-cutting ants in the higher attine fungus-growing ant symbiosis.

Fungus-gardening (attine) ants grow fungus for food in protected gardens, which contain beneficial, auxiliary microbes, but also microbes harmful to gardens. Among these potentially pathogenic microorganisms, the most consistently isolated are fungi in the genus Escovopsis, which are thought to co-evolve with ants and their cultivar in a tripartite model. To test clade-to-clade correspondence between Escovopsis and ants in the higher attine symbiosis (including leaf-cutting and non-leaf-cutting ants), we amassed a geographically comprehensive collection of Escovopsis from Mexico to southern Brazil, and reconstructed the corresponding Escovopsis phylogeny. Contrary to previous analyses reporting phylogenetic divergence between Escovopsis from leafcutters and Trachymyrmex ants (non-leafcutter), we found no evidence for such specialization; rather, gardens from leafcutters and non-leafcutters genera can sometimes be infected by closely related strains of Escovopsis, suggesting switches at higher phylogenetic levels than previously reported within the higher attine symbiosis. Analyses identified rare Escovopsis strains that might represent biogeographically restricted endemic species. Phylogenetic patterns correspond to morphological variation of vesicle type (hyphal structures supporting spore-bearing cells), separating Escovopsis with phylogenetically derived cylindrical vesicles from ancestral Escovopsis with globose vesicles. The new phylogenetic insights provide an improved basis for future taxonomic and ecological studies of Escovopsis.

Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states.

Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, and viviparity has evolved many times independently within amniotes (especially in lizards and snakes), with possibly a few reversions to oviparity. In amniotes, the shelled egg is considered a complex structure that is unlikely to re-evolve if lost (i.e., it is an example of Dollo's Principle). However, a recent ancestral state reconstruction analysis concluded that viviparity was the ancestral state of squamate reptiles (lizards and snakes), and that oviparity re-evolved from viviparity many times throughout the evolutionary history of squamates. Here, we re-evaluate support for this provocative conclusion by testing the sensitivity of the analysis to model assumptions and estimates of squamate phylogeny. We found that the models and methods used for parity mode reconstruction are highly sensitive to the specific estimate of phylogeny used, and that the point estimate of phylogeny used to suggest that viviparity is the root state of the squamate tree is far from an optimal phylogenetic solution. The ancestral state reconstructions are also highly sensitive to model choice and specific values of model parameters. A method that is designed to account for biases in taxon sampling actually accentuates, rather than lessens, those biases with respect to ancestral state reconstructions. In contrast to recent conclusions from the same data set, we find that ancestral state reconstruction analyses provide highly equivocal support for the number and direction of transitions between oviparity and viviparity in squamates. Moreover, the reconstructions of ancestral parity state are highly dependent on the assumptions of each model. We conclude that the common ancestor of squamates was oviparous, and subsequent evolutionary transitions to viviparity were common, but reversals to oviparity were rare. The three putative reversals to oviparity with the strongest phylogenetic support occurred in the snakes Eryx jayakari and Lachesis, and the lizard, Liolaemus calchaqui. Our results emphasize that because the conclusions of ancestral state reconstruction studies are often highly sensitive to the methods and assumptions of analysis, researchers should carefully consider this sensitivity when evaluating alternative hypotheses of character-state evolution.

Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data.

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of likelihood-based models for the estimation of phylogeny from discrete morphological data exist, especially for the Mk model of discrete character evolution. Here we explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, we describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity.