Tree thinking cannot taken for granted: challenges for teaching phylogenetics.
Ontology highlight
ABSTRACT:
SUBMITTER: Sandvik H
PROVIDER: S-EPMC2254468 | biostudies-other | 2008 Mar
REPOSITORIES: biostudies-other
Similar Datasets
Project description:The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking curriculum or business-as-usual instruction. We found greater gains in tree-thinking abilities for the experimental instruction group than for the business-as-usual group, as measured by performance on our novel assessment instrument. This was a medium size effect. These gains were observed on an unannounced test that was administered ∼5-6 weeks after the primary instruction in tree thinking. The nature of students' postinstruction difficulties with tree thinking suggests that the critical underlying concept for acquiring expert-level competence in this area is understanding that any specific phylogenetic tree is a subset of the complete, unimaginably large ToL.
| S-EPMC5132363 | biostudies-literature
Project description:BackgroundDeveloping a public health workforce that can understand problems from a population perspective is essential in the design of impactful user-centred responses to current population health challenges. Design Thinking, a user-driven process for problem-defining and solution-finding, not only has utility in the field of public health but stands as a potential mechanism for developing critical skills -such as empathy, creativity and innovation- amongst future professionals. Though the literature reflects the use of DT across many health sciences disciplines, less research has been published on how students apply learned concepts using real-world challenges of their choice and what difficulties they face during the process.MethodsThis case study evaluates achieved learning outcomes after the introduction of a design thinking block into post-graduate public health curriculum at the University College Dublin. Two independent assessors evaluated student learning outcomes and observed difficulties during the process by assessing group presentations to identify and understand any learning difficulties using an ad-hoc designed tool. The tool consisted of twelve items scored using a 5-point Likert scale. Student feedback, in the form of an online survey, was also analysed to determine their level of enjoyment, perceived learning outcomes and opinions on the course content.ResultsThe assessors evaluated thirteen DT group presentations and reports from 50 students. The groups chose a range of topics from socialization of college students during Covid-19 to mental health challenges in a low-income country. Independent assessment of assignments revealed that the highest scores were reached by groups who explored a challenge relevant to their own lives (more than 80% of total possible points versus 60% class average). The groups that explored challenges more distant to themselves struggled with problem finding with a mean score of 2.05 (SD ± 1.2) out of 5 in that domain. The greatest difficulties were observed in problem finding and ideation. Though most students found the design thinking block enjoyable and relevant to their education, they recommended that the DT block be a stand-alone module. Students recognized that groups who chose a familiar topic experienced fewer difficulties throughout the process.ConclusionThe study showed that DT learning outcomes were best achieved when students focused on challenges, they had either personally experienced or were familiar with. These findings provide insight for future iterations of DT workshops and support the teaching of user-centred approaches to future public health practitioners.
| S-EPMC9002025 | biostudies-literature
Project description:Darwin described evolution as "descent with modification." Descent, however, is not an explicit focus of most evolution instruction and often leaves deeply held misconceptions to dominate student understanding of common ancestry and species relatedness. Evolutionary trees are ways of visually depicting descent by illustrating the relationships between species and groups of species. The ability to properly interpret and use evolutionary trees has become known as "tree thinking." We used a 20-question assessment to measure misconceptions in tree thinking and compare the proportion of students who hold these misconceptions in an introductory biology course with students in two higher-level courses including a senior level biology course. We found that misconceptions related to reading the graphic (reading the tips and node counting) were variably influenced across time with reading the tips decreasing and node counting increasing in prevalence. On the other hand, misconceptions related to the fundamental underpinnings of evolutionary theory (ladder thinking and similarity equals relatedness) proved resistant to change during a typical undergraduate study of biology. A possible new misconception relating to the length of the branches in an evolutionary tree is described. Understanding the prevalence and persistence of misconceptions informs educators as to which misconceptions should be targeted in their courses.
| S-EPMC5134942 | biostudies-literature
Project description:BackgroundSince Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.ResultsHeat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer.ConclusionOur phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.
| S-EPMC1156881 | biostudies-literature
Project description:We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.
| S-EPMC5559066 | biostudies-literature
Project description:The tendency to discretize biology permeates taxonomy and systematics, leading to models that simplify the often continuous nature of populations. Even when the assumption of panmixia is relaxed, most models still assume some degree of discrete structure. The multispecies coalescent has emerged as a powerful model in phylogenetics, but in its common implementation is entirely space-independent - what we call the "missing z-axis". In this article, we review the many lines of evidence for how continuous spatial structure can impact phylogenetic inference. We illustrate and expand on these by using complex continuous-space demographic models that include distinct modes of speciation. We find that the impact of spatial structure permeates all aspects of phylogenetic inference, including gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by utilizing our results to suggest how researchers can identify spatial structure in phylogenetic datasets.
| S-EPMC10289471 | biostudies-literature
Project description:Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel's λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.
| S-EPMC4481530 | biostudies-literature
Project description:A growing body of literature highlights the increasing demand on college graduates to possess the problem finding, problem framing, and problem-solving skills necessary to address complex real-world challenges. Design thinking (DT) is an iterative, human-centered approach to problem solving that synthesizes what is desirable, equitable, technologically feasible, and sustainable. As universities expand efforts to train students with DT mindsets and skills, we must assess faculty and student DT practices and outcomes to better understand DT course experiences. Understanding how DT is taught and experienced within higher education can help schools promote student learning and align their training programs with professional, personal, and civic needs. In this study, surveys were completed by 19 faculty and 196 students from 23 courses at four universities. DT teaching and learning was characterized by three DT practices and five outcomes. Statistically significant differences were found by discipline of study and student type (i.e., graduate vs undergraduate), but not by gender or race/ethnicity. These results can be used to inform the development of classroom-based DT teaching and learning strategies across higher education institutions and disciplines.
| S-EPMC8947127 | biostudies-literature
Project description:Food Microbiology is included in majors such as Food Engineering, Food Science and Technology, Nutrition, Veterinary Medicine, Gastronomy, Pharmaceutical Sciences, among others. Food safety and hygiene are usually the focus, but the technological applications of microbes through fermentations are also covered. During an education symposium at the Brazilian Congress of Microbiology in 2017, a group of professors expressed their difficulties associated with teaching to new generations, the use of technology in the classroom, and the application of new learning tools. The objective of this study was to gather information about the educational practices among Brazilian professors who teach Food Microbiology throughout the country. The results indeed confirmed the diversity of careers in which food microbiology is taught. We verified that professors mixed traditional teaching strategies with modern active learning methods, even though some difficulties associated with lack of time, pedagogical training, and low adherence of students for adopting these modern methods were commonly highlighted. The preferred teaching approaches were dialogued or discussed lectures, seminars, homework, case studies, and field visits. It is noteworthy that most professors still use traditional teaching methods. It is crucial that awareness concerning the educational needs in different careers and the challenges and dilemmas facing education for the new generations should be dealt with by using effective teaching approaches in food microbiology education. We suggest that a more permanent discussion forum among faculty members dealing with food microbiology in the country should be launched and this work is a step towards this goal.
| S-EPMC7058747 | biostudies-literature
Project description:Characteristics and outcomes of tree nut (TN) oral food challenges (OFCs) in patients with TN allergy or sensitization alone are poorly studied.To determine the relation between TN sensitization levels and OFC outcomes.Open TN OFCs performed from 2007 through 2015 at a referral center were analyzed to compare outcome based on skin prick test (SPT) wheal size, food-specific immunoglobulin E (sIgE), peanut co-allergy, and TN sensitization only vs TN allergy with sensitization to other TNs. Delayed OFC was defined as longer than 12 months from the time of an sIgE level lower than 2 kUA/L.Overall passage rate was 86% for 156 TN OFCs in 109 patients (54 almond, 28 cashew, 27 walnut, 18 hazelnut, 14 pecan, 13 pistachio, and 2 Brazil nut). Passage rates were 76% (n = 67) in patients with a history of TN allergy who were challenged to another TN to which they were sensitized and 91% (n = 65) in those with TN sensitization only (mean sIgE 1.53 kUA/L; range 0.35-9.14). Passage rates were 89% (n = 110 of 124) for a TN sIgE level lower than 2 kUA/L and 69% (11 of 16) for a TN sIgE level of at least 2 kUA/L. In 44 challenges in patients with peanut allergy and TN co-sensitization, the TN OFC passage rate was 96%. In 41 TN OFCs with a TN SPT wheal size of at least 3 mm, 61% passed, with a mean wheal size of 4.8 mm (range 3-11) in those passing vs 9 mm (range 3-20) in those failing.TN challenges are frequently passed in patients with TN sensitization with or without a history of TN reactivity despite a TN SPT wheal of at least 3 mm or a TN sIgE level of at least 2 kUA/L. Nearly all patients with peanut allergy and TN co-sensitization passed the TN challenge, questioning the clinical relevance of "co-allergy."
| S-EPMC6085138 | biostudies-literature