Untangling the contribution of characters to evolutionary relationships: a case study using fossils,morphology, and Genes

Given the importance of phylogenetic trees to understanding common ancestry and evolution, they are a necessary part of the undergraduate biology curriculum. However, a number of common misconceptions, such as reading across branch tips and understanding homoplasy, can pose difficulties in student understanding. Students also may take phylogenetic trees to be fact, instead of hypotheses. Below we outline a case study that we have used in upper-level undergraduate evolution and ichthyology courses that utilizes shark teeth (representing fossils), body characters, and mitochondrial genes. Students construct their own trees using freely available software, and are prompted to compare their trees with a series of questions. Finally, students explore homoplasy, polytomies, and trees as hypotheses during a class discussion period. This case study gives students practice with tree-thinking, as well as demonstrating that tree topology is reliant on which characters and tree-building algorithms are used.     

Teaching Tree-Thinking to Undergraduate Biology Students

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.     

Teaching Tree Thinking to College Students: It’s Not as Easy as You Think

The ability to understand and reason with tree-of-life diagrams (i.e., cladograms), referred to as tree thinking, is an essential skill for biology students. Yet, recent findings indicate that cladograms are cognitively opaque to many college students, leading them to misinterpret the information depicted. The current studies address the impact of prior biological background and instruction in phylogenetics on students?? competence at two foundational tree-thinking skills. In Study 1, college students with stronger (N?=?52) and weaker (N?=?60) backgrounds in biology were asked to (a) identify all the nested clades in two cladograms and (b) evaluate evolutionary relatedness among taxa positioned at different hierarchical levels (two questions) and included in a polytomy (two questions). Stronger-background students were more successful than weaker-background students. In Study 2, a subset of the stronger-background students (N?=?41) who were enrolled in an evolution class subsequently received two days of instruction on phylogenetics. As expected, these students?? tree-thinking skills generally improved with instruction. However, although these students did very well at marking the nested clades, fundamental misinterpretations of relative evolutionary relatedness remained. The latter was especially, although not exclusively, the case for taxa included in a polytomy. These results highlight the importance of teaching cladistics, as well as the need to tailor such instruction to the difficulties students have learning key macroevolutionary concepts.     

Teaching tree thinking in an upper level organismal biology course: testing the effectiveness of a multifaceted curriculum

The ability to interpret and reason from Tree of Life diagrams is a key component of twenty-first century science literacy. This article reports on the authors’ continued development of a multifaceted research-based curriculum – including an instructional booklet, lectures, laboratories and a field activity – to teach such tree thinking to biology students. Results are presented from a study involving biology students enrolled in an upper level organismal biology class. All students received the multi-week tree-thinking curriculum, and learning was assessed by comparing pretest and posttest scores on the novel tree-thinking assessment instrument developed by the authors. Quantitatively, the authors found large gains in tree-thinking abilities due to their instruction. The results also provided qualitative evidence that the authors succeeded in their more general goal of helping students to appreciate the interconnectedness of Earth’s biodiversity through the utility of phylogenetic trees.     

Using Inquiry and Tree-Thinking to “March Through the Animal Phyla”: Teaching Introductory Comparative Biology in an Evolutionary Context

Biodiversity was originally taught in our Introductory Organismal Biology course at Michigan State University (LB144; freshman/sophomore majors) by rote memorization of isolated facts about organisms. When we moved to an inquiry-based laboratory framework to improve pedagogy, an unfortunate and unforeseen result was the loss of much of our study of biodiversity. In this paper, we describe the restructuring of LB144 to restore the study of biodiversity and organismal groups while retaining the benefits of an inquiry-based approach. The curricular intervention was accomplished through the creation and implementation of a four-week Comparative Biology laboratory stream. During this stream, student research teams recorded and organized observations that they made on a range of organisms and analyzed their data in a phylogenetic framework. During the stream, our students worked through a set of exercises designed to help them learn how to read, interpret, and manipulate phylogenetic trees. We placed particular emphasis on the concept that phylogenetic trees are hypotheses of relationship that can be tested with scientific data. This incorporation of phylogenies and phylogenetic analysis, or “tree-thinking,” into our students’ work provided an explicit synthetic evolutionary framework for their comparative biodiversity studies. End-of-stream products included a team phylogenetic analysis exercise and an individual comparative biology oral presentation.     

A valid assessment of students’ skill in determining relationships on evolutionary trees

Background

Evolutionary trees illustrate relationships among taxa. Interpreting these relationships requires developing a set of “tree-thinking” skills that are typically included in introductory college biology courses. One of these skills is determining relationships among taxa using the most recent common ancestor, yet many students instead use one or more alternate strategies to determine relationships. Several alternate strategies have been well documented and these include using superficial similarity, proximity at the tips of a tree, or the fewest intervening nodes in the tree to group taxa.

Results

We administered interviews (n = 16) and pencil-and-paper questionnaires (n = 205), and constructed a valid and reliable assessment that measured how well students determined relationships among taxa on an evolutionary tree. Our questions asked students to consider a focal taxon and identify which of two additional taxa is most closely related to it. We paired the use of most recent common ancestor with one of three alternative strategies (i.e., similarity, proximity, or node-counting) to explicitly test students’ understanding of the relationships among the taxa on each tree.

Conclusions

Our assessment enables us to identify students who are effectively distracted by an alternative strategy, those who use the most recent common ancestor inconsistently, or who are guessing in order to determine relationships among taxa. Our 18-question tool (see Additional file 1) can be used for formative assessment of student understanding of how to interpret relationships on evolutionary trees. Because our assessment tests for the same skill throughout, students who answer incorrectly, even once, likely have an incomplete understanding of how to determine relationships on evolutionary trees and should receive follow-up instruction.

     

Student construction of phylogenetic trees in an introductory biology course

Background

Phylogenetic trees have become increasingly essential across biology disciplines. Consequently, learning about phylogenetic trees has become an important component of biology education and an area of interest for biology education research. Construction tasks, in which students generate phylogenetic trees from some type of data, are often used for instruction. However, the impact of these exercises on student learning is uncertain, in part due to our fragmented knowledge of what students construct during the tasks. The goal of this project was to develop a more robust method for describing student-generated phylogenetic trees, which will support future investigations that attempt to link construction tasks with student learning.

Results

Through iterative examination of data from an introductory biology course, we developed a method for describing student-generated phylogenetic trees in terms of style, conventionality, and accuracy. Students used the diagonal style more often than the bracket style for construction tasks. The majority of phylogenetic trees were constructed conventionally, and variable orientation of branches was the most common unconventional feature. In addition, the majority of phylogenetic trees were generated correctly (no errors) or adequately (minor errors only) in terms of accuracy. Suggesting extant taxa are descended from other extant taxa was the most common major error, while empty branches and extra nodes were very common minor errors.

Conclusions

The method we developed to describe student-constructed phylogenetic trees uncovered several trends that warrant further investigation. For example, while diagonal and bracket phylogenetic trees contain equivalent information, student preference for using the diagonal style could impact comprehension. In addition, despite a lack of explicit instruction, students generated phylogenetic trees that were largely conventional and accurate. Surprisingly, accuracy and conventionality were also dependent on each other. Our method for describing phylogenetic trees constructed by students is based on data from one introductory biology course at one institution, and the results are likely limited. We encourage researchers to use our method as a baseline for developing a more generalizable tool, which will support future investigations that attempt to link construction tasks with student learning.

     

The assembly of tropical tree communities – the advances and shortcomings of phylogenetic and functional trait analyses

Tropical tree communities present one of the most challenging systems for studying the processes underlying community assembly. Most community assembly hypotheses consider the relative importance of the ecological similarity of co‐occurring species. Quantifying this similarity is a daunting and potentially impossible task in species‐rich assemblages. During the past decade tropical tree ecologists have increasingly utilized phylogenetic trees and functional traits to estimate the ecological similarity of species in order to test mechanistic community assembly hypotheses. A large amount of work has resulted with many important advances having been made along the way. That said, there are still many outstanding challenges facing those utilizing phylogenetic and functional trait approaches to study community assembly. Here I review the conceptual background, major advances and major remaining challenges in phylogenetic‐ and trait‐based approaches to community ecology with a specific focus on tropical trees. I argue that both approaches tremendously improve our understanding of tropical tree community ecology, but neither approach has fully reached its potential thus far.     

Recovering speciation and extinction dynamics based on phylogenies

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.     

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

The advent and maturation of algorithms for estimating species trees—phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes—represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long‐standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a “local optimum” for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term “phylogeny” for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.     

Phylogenetic Structure of Tree Species across Different Life Stages from Seedlings to Canopy Trees in a Subtropical Evergreen Broad-Leaved Forest

Investigating patterns of phylogenetic structure across different life stages of tree species in forests is crucial to understanding forest community assembly, and investigating forest gap influence on the phylogenetic structure of forest regeneration is necessary for understanding forest community assembly. Here, we examine the phylogenetic structure of tree species across life stages from seedlings to canopy trees, as well as forest gap influence on the phylogenetic structure of forest regeneration in a forest of the subtropical region in China. We investigate changes in phylogenetic relatedness (measured as NRI) of tree species from seedlings, saplings, treelets to canopy trees; we compare the phylogenetic turnover (measured as β_NRI) between canopy trees and seedlings in forest understory with that between canopy trees and seedlings in forest gaps. We found that phylogenetic relatedness generally increases from seedlings through saplings and treelets up to canopy trees, and that phylogenetic relatedness does not differ between seedlings in forest understory and those in forest gaps, but phylogenetic turnover between canopy trees and seedlings in forest understory is lower than that between canopy trees and seedlings in forest gaps. We conclude that tree species tend to be more closely related from seedling to canopy layers, and that forest gaps alter the seedling phylogenetic turnover of the studied forest. It is likely that the increasing trend of phylogenetic clustering as tree stem size increases observed in this subtropical forest is primarily driven by abiotic filtering processes, which select a set of closely related evergreen broad-leaved tree species whose regeneration has adapted to the closed canopy environments of the subtropical forest developed under the regional monsoon climate.     

Backyard evolutionary biology: Investigating local flowers brings learning to life

Inquiry‐based learning allows students to actively engage in and appreciate the process of science. As college courses transition to online instruction in response to COVID‐19, incorporating inquiry‐based learning is all the more essential for student engagement. However, with the cancelation of in‐person laboratory courses, implementing inquiry can prove challenging for instructors. Here, I describe a case that exemplifies a strategy for inquiry‐based learning and can be adapted for use in various course modalities, from traditional face‐to‐face laboratory courses to asynchronous and synchronous online courses. I detail an assignment where students explore the developmental basis of morphological evolution. Flowers offer an excellent example to address this concept and are easy for students to access and describe. Students research local flowering plants, collect and dissect flower specimens to determine their whorl patterns, and generate hypotheses to explain the developmental genetic basis of the patterns identified. This task allows students to apply their scientific thinking skills, conduct guided exploration in nature, and connect their understanding of the developmental basis of evolutionary change to everyday life. Incorporating inquiry using readily available, tangible, tractable real‐world examples represents a pragmatic and effective model that can be applied in a variety of disciplines during and beyond COVID‐19.     

互助学习在科技学院护理专业组胚教学中的尝试

目的探讨互助学习在医学专业科技学院教学中的应用效果。方法对我校科技学院2009级护理专业组胚实验教学中实施互助学习,课程结束后对学生进行成绩分析及问卷调查。结果通过互助学习学生成绩显著提高,语言表达能力、合作能力、分析解决问题能力相应增强。结论互助学习能激发学生学习兴趣,提高学习能力和实验技能,改善学生的综合素质,为科技学院学生因材施教寻找到有效教学模式。     

New approaches to phylogenetic tree search and their application to large numbers of protein alignments

Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.     

The Effect of Active Learning Methodologies on the Teaching of Pharmaceutical Care in a Brazilian Pharmacy Faculty

BackgroundIn recent years, pharmacists have been involved in expanded patient care responsibilities, for example patient counseling in self-medication, medication review and pharmaceutical care, which require graduates to develop the necessary competences. Consequently, reorientation of pharmacy education has become necessary. As such, active learning strategies have been introduced into classrooms to increase problem-solving and critical thinking skills of students. The objective of this study was to evaluate the performance and perceptions of competency of students in a new pharmaceutical care course that uses active learning methodologies.MethodsThis pharmaceutical care course was conducted in the first semester of 2014, in the Federal University of Sergipe. In the pharmaceutical care course, active learning methods were used, consisting of dialogic classroom expository, simulation and case studies. Student learning was evaluated using classroom tests and instruments that evaluated the perception of competency in pharmaceutical care practice. Furthermore, students'' satisfaction with the course was evaluated.ResultsThirty-three students completed the four evaluations used in the course (i.e., a discursive written exam, seminars, OSCE, and virtual patient); 25 were female (75.75%), and the median age was 23.43 (SD 2.82) years. The overall mean of student scores, in all evaluation methods was 7.97 (SD 0.59) on a scale of 0 to 10 points, and student performance on the virtual patient method was statistically superior to other methods. With respect to the perception of competency in pharmaceutical care practice, a comparison of pre- and post-test scores revealed statistically significant improvement for all evaluated competences. At the end of the semester, the students presented positive opinions of the pharmaceutical care course.ConclusionsThe results suggest that an active learning course can enhance the learning of pharmaceutical care competences. In future studies it will be necessary to compare active learning to traditional methods.     

Training in medical informatics. The use of computers for diagnostic purposes

Part of a blockcourse on medical informatics is presented; this course is intended for medical students. It is shown how medical students are introduced to the study of the role of computers for diagnostic purposes. The course consists of an oral presentation which introduces the student to the subject, and of practical work on systems in order to more fully comprehend the topics explained in the oral part of the blockcourse. In the oral presentation the student is introduced to various concepts that are used in computer-aided diagnosis. A critical review of the possibilities of computer use for diagnostic purposes is given. A system is presented, with which the student can work interactively. It consists of a database of patients, referred to the hospital because of suspected congenital heart disorder. Bayes' rule and diagnostic tree decision schemes are available to the student to acquaint himself with the subject. The ways he can work with this system are explained. The course is given regularly (every 4 months) to medical students and is well appreciated.     

Evolution and nature of science instruction

In this article, I provide an analysis of my work (1985–present) with non-major biology students and science teacher candidates in developing strategies for teaching and enhancing learning with respect to evolutionary science. This first-person account describes changes in evolution instruction over the course of a career based on personal experiences, research-informed practices, and a critical collaboration with colleague Mike U. Smith. I assert four insights concerning the influence and efficacy of teaching nature of science (NOS) prior to the introduction of evolution within college courses for science non-majors and science teacher candidates. These insights are: (a) teach explicit NOS principles first; (b) integrate evolution as a theme throughout a course in introductory biology (but after NOS principles have been introduced); (c) use active learning pedagogies; and (d) use non-threatening alternative assessments to enhance student learning and acceptance of evolutionary science. Together, these insights establish a pedagogy that I (and my colleagues) have found to be efficacious for supporting novice students as they engage in the study of evolutionary science.     

Tree thinking cannot taken for granted: challenges for teaching phylogenetics

Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how to read evolutionary trees. Possible causes and implications of this mental bias are discussed. It seems that biological textbooks can be an important source of confusion for students. While group and developmental thinking have disappeared from most textual representations of evolution, they have survived in the evolutionary tree drawings of many textbooks. It is quite common for students to encounter anthropocentric trees and even trees containing stem groups and paraphyla. While these biases originate from the unconscious philosophical assumptions made by authors, the findings suggest that presenting unbiased evolutionary trees in biological publications is not merely a philosophical virtue but has also clear practical implications.

Introducing student inquiry in large introductory genetics classes

An appreciation of genetic principles depends upon understanding the individual curiosity that sparked particular investigations, the creativity involved in imagining alternative outcomes and designing experiments to eliminate these outcomes, and the clarity of thought necessary to convince one's scientific peers of the validity of the conclusions. At large research universities, students usually begin their study of genetics in large lecture classes. It is widely assumed that the lecture format, coupled with the pressures to be certain that students become familiar with the principal conclusions of genetics investigations, constrains most if not all departures from the formats textbooks used to explain these conclusions. Here I present several examples of mechanisms to introduce meaningful student inquiry in an introductory genetics course and to evaluate student creative effort. Most of the examples involve altered student preparation prior to class and additional in-class activities, while a few depend upon a smaller recitation section, which accompanies the course from which the examples have been drawn. I conclude that large introductory classes are suitable venues to teach students how to identify scientific claims, determine the evidence that is essential to eliminate alternative conclusions, and convince their peers of the validity of their arguments.     

GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication,Transfer, and Loss

Inferring phylogenetic trees for individual homologous gene families is difficult because alignments are often too short, and thus contain insufficient signal, while substitution models inevitably fail to capture the complexity of the evolutionary processes. To overcome these challenges, species-tree-aware methods also leverage information from a putative species tree. However, only few methods are available that implement a full likelihood framework or account for horizontal gene transfers. Furthermore, these methods often require expensive data preprocessing (e.g., computing bootstrap trees) and rely on approximations and heuristics that limit the degree of tree space exploration. Here, we present GeneRax, the first maximum likelihood species-tree-aware phylogenetic inference software. It simultaneously accounts for substitutions at the sequence level as well as gene level events, such as duplication, transfer, and loss relying on established maximum likelihood optimization algorithms. GeneRax can infer rooted phylogenetic trees for multiple gene families, directly from the per-gene sequence alignments and a rooted, yet undated, species tree. We show that compared with competing tools, on simulated data GeneRax infers trees that are the closest to the true tree in 90% of the simulations in terms of relative Robinson–Foulds distance. On empirical data sets, GeneRax is the fastest among all tested methods when starting from aligned sequences, and it infers trees with the highest likelihood score, based on our model. GeneRax completed tree inferences and reconciliations for 1,099 Cyanobacteria families in 8 min on 512 CPU cores. Thus, its parallelization scheme enables large-scale analyses. GeneRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax (last accessed June 17, 2020).