Topics In Evolution Research Articles

DEDC-IMAE: A deep evolutionary document clustering model with inherited mixed autoencoder

Recently, deep document clustering has been increasingly attracting interest. However, the design of existing deep document clustering methods is limited to processing only static document datasets because applying these methods to dynamic text documents is challenging as the underlying topics of document datasets are not static but evolve. Deep models must learn the cluster-level representations that are inherited. Thus, methods must be explored to implement the inheritance of cluster-level representations. In this study, we overcome the aforementioned challenges and propose a deep evolutionary document clustering model with an inherited mixed autoencoder (DEDC-IMAE), to discover evolutionary document structures with evolutionary topics in dynamic document datasets. An inherited mixed autoencoder (IMAE) is designed to learn an evolutionary semantic representation of each document considering both the inherited historical topic semantics and the document's own characteristics, to reflect the evolved topic semantics. Using the document evolutionary semantics, a deep evolutionary document clustering (DEDC) module is then investigated to learn a clustering partition that reflects the characteristics of document datasets. Experimental results on a real evolutionary text document dataset showed that DEDC-IMAE achieves better evolutionary clustering results than a variety of baseline models.

On the presence of the epibiont (ectosymbiont) Lagenophrys lenticulata (Kellicott, 1885) (Ciliophora) on Hyalella cursvispina Schoemaker, 1942: is it possible to find it on Chilean Hyalella populations?

Abstract The amphipods of the genus Hyalella have many endemic species throughout South America, and these may have poorly studied associated species as epibionts. The aim of the present study was to review the literature on the presence of the protozoon Lagenophrys lenticulata (Kellicott, 1885) on species of Hyalella and contrast the results with the geographical distribution of the reported hosts. The literature records the presence of L. lenticulata on populations of H. azteca from Canada, Mexico and the United States of America, and on populations of H. curvispina from Uruguay. The literature also reports that H. curvispina is widespread throughout southern South America, including Argentina and Chile, and that it would be possible to find the presence of epibionts on other populations of H. curvispina. The corresponding biogeographical and evolutionary topics are discussed.

A review of ectocommensals and parasites of Chilean crayfishes (Decapoda, Parastacidae), with emphasis on Temnocephala chilensis (Moquin-Tandon, 1846) (Platyhelminthes)

Abstract The crayfishes of Chile are endemic species and have been poorly studied with respect to their biology. The available literature is restricted to species descriptions, whereas there is no information about other biological topics such as ectocommensals and parasites, which can affect crayfishes. The aim of the present study was to do a literature review and update the information about ectocommensals and parasites that have been reported from Chilean crayfishes. The literature mentioned the presence of Temnocephala chilensis (Platyhelminthes), Stratiodrilus pugnaxi (Polychaeta) and Protozoa such as species of the genera Operculigera and Lagenophrys as ectocommensals for Parastacus pugnax and Samastacus spinifrons. As an endoparasite, Psorospermium haeckelii was reported, a unicellular eukaryotic organism that was found in P. pugnax ovaria. An additional analysis of collected specimens of P. pugnax and S. spinifrons revealed the presence of T. chilensis, albeit at a low incidence. Ecological, biogeographical and evolutionary topics are discussed considering the case of a marked microendemism of an organism associated with Chilean crayfishes.

BioInteractive’s Free Online Professional Learning Course on Evolution

Teachers are eager for professional development on teaching evolution, especially if it includes direct ties to relevant curricula and detailed lesson plans. Howard Hughes Medical Institute’s BioInteractive Online Professional Learning: Evolution course was developed to provide educators with free, in-depth, multimedia resources that highlight important scientific concepts and studies in evolution and engage participants through interactive activities that link to student resources. Our goals in the development of the asynchronous, nonfacilitated course were to (1) deepen teachers’ content knowledge of evolutionary concepts essential to NGSS and AP Biology courses, (2) increase teachers’ confidence and comfort in teaching evolution content to general biology and AP Biology students, (3) have teachers identify major evolutionary concepts in scientific studies, authentic data, or educational media used to teach evolution, and (4) assist teachers in identifying and incorporating relevant BioInteractive resources to illustrate evolutionary content and science practices in their own course(s). Our results from a postcourse survey that included pre-post retrospective confidence questions suggest that the course improved educators’ knowledge in evolution and their confidence in teaching evolutionary topics. Overall, this course provides educators the opportunity to deepen their content knowledge and obtain exciting, relevant, and reliable resources to use in their classrooms.

Is knowledge of evolution useful? A mixed methods examination of college biology students’ views

ABSTRACT This mixed methods study explores college biology students’ perceptions of the utility of evolution knowledge. In Phase I, 14 college biology students from an upper-level Evolution course were interviewed about their evolution acceptance and perceptions of the utility of evolutionary knowledge. In Phase II, findings from Phase I were used to develop a 28-item quantitative Usefulness of Evolution Knowledge Survey. Then, 472 college biology students enrolled in three biology courses were given the Usefulness of Evolution Knowledge survey to identify (1) evolution topics that have the highest utility value for evolution learners, (2) careers for which evolution knowledge is deemed most useful, and (3) relationships among evolution utility value and other constructs. The most useful evolutionary topics were genetic variation and adaptations of particular organisms to particular environments. Evolutionary knowledge was deemed most useful for conservation careers, with less utility for medical and forensic careers, and far less utility for careers in physics or chemistry. Significant relationships were found between perceptions of the usefulness of evolution and evolution acceptance, understanding of evolution, and intended career. Findings are discussed within the framework of the Expectancy Value Theory, and implications for future pedagogical interventions and associated research are provided.

Escape Zoom!: Reviewing Introductory Evolution Content Using an Escape Room Format

Reviewing and integrating key concepts and learning goals at the end of a biology course can be overwhelming to students and instructors alike. Often end-of-term review sessions in preparation for final exams are heavily based on memorization, and content coverage may be favored over students&rsquo; deeper understanding of fewer key ideas. We developed a final exam review for a virtual introductory evolution course using an &ldquo;escape room&rdquo; format, which consisted of unique activities&mdash;including puzzles, role-playing, and literature searches&mdash;aligned with course learning goals. Similar to a traditional escape room, students needed to collaboratively solve or complete each activity before moving on to the subsequent task. Our escape room activity was conducted virtually via Zoom and included both whole-class and smaller breakout room interactions. We recommend instructors utilize escape rooms as an engaging and effective way to review key concepts in their courses. <em>Primary image:&nbsp;</em>Virtual Escape Room. In our activity, students virtually engage in activities related to evolutionary topics such as cichlid speciation, mRNA COVID-19 vaccines, and extinction, among others. All images used in this image are open source, and associated links for all images are listed here:&nbsp;<a href="https://unsplash.com/photos/smgTvepind4">https://unsplash.com/photos/smgTvepind4</a>, <a href="https://unsplash.com/photos/4_hFxTsmaO4">https://unsplash.com/photos/4_hFxTsmaO4</a>, <a href="https://unsplash.com/photos/_BJVJ4WcV1M">https://unsplash.com/photos/_BJVJ4WcV1M</a>, <a href="https://unsplash.com/photos/k0KRNtqcjfw">https://unsplash.com/photos/k0KRNtqcjfw</a>, <a href="https://unsplash.com/photos/Pitb97HIn6Y">https://unsplash.com/photos/Pitb97HIn6Y</a>

Evolutionary Content Knowledge, Religiosity and Educational Background of Slovene Preschool and Primary School Pre-Service Teachers

Evolution by natural selection is the fundamental backbone of the life sciences. Therefore, it is important for teacher education programs to ensure graduates possess a strong knowledge of evolution in order to teach at all levels of biology education. The main aim was to investigate the impacts of the Slovene pre-service preschool and primary school teachers’ religiosity and educational background on their evolutionary content knowledge. In the present study, understanding of five evolutionary topics, religiosity and educational background of 269 students was studied. Results show that students have a very poor understanding of evolution. They very often use teleological reasoning. Although many pieces of research have shown that religiosity can be in conflict with evolutionary theory, our findings show that religiosity does not significantly correlate with evolutionary knowledge nor to the educational background of students. However, for students’ understanding of evolution, it is important how many years of biology lessons they had in secondary school. This should be better taken into account by educational policymakers because evolutionary principles are becoming increasingly relevant in medicine, agriculture and other socio-scientific topics.

Examining Reasoning Practices and Epistemic Actions to Explore Students’ Understanding of Genetics and Evolution

This article focuses on students’ discursive moves and reasoning practices while engaged in a task that requires making explanatory links between sickle cell disease and malaria. Both diseases pertain to key areas of the biology curriculum, namely, genetic variability and natural selection, and are connected to the theory of evolution of living organisms. Specifically, this study examines the intersections among rhetoric, argumentation and epistemic actions in supporting students’ understanding of complex biological dynamics, which are interlinked across time and space, but are often addressed separately in the curriculum. Data were collected over the course of two school years (2014–2016) with a group of 20 15–17-year-old students and their biology teacher. The findings indicate that while rhetorical moves helped students mobilize data, the use of evidence to support claims remained limited. Conversely, the type of epistemic actions enacted by the students appears to be directly related to the type of data being analysed. Hence, rhetorical moves in combination with argumentation practices appear to account for students’ differential performances in building more complex explanations of evolutionary topics. We conclude that further understanding of reasoning practices and how these are shaped by discursive moves is required in biology education, in order to help students view biological processes in a wider context, and thus gain a better understanding of evolutionary phenomena.

A community-informed list of key speciation concepts for undergraduate education

BackgroundMany topics in evolutionary biology have been the focus of little research about student thinking and learning. This lack of research limits the evidence base on which instructors can draw to inform their teaching. A key starting place for education research about evolutionary topics is determining what concepts are important for undergraduates to learn. This work develops a community-informed list of key concepts about speciation. Speciation is commonly taught in undergraduate biology education, yet has been the focus of almost no research on teaching and learning. We gathered input from over 110 evolution educators and speciation researchers to create a comprehensive list of speciation concepts for undergraduate education.ResultsThe community-informed list includes 24 concept statements organized within 4 overarching concepts. At least 80% of experts rated these statements as scientifically accurate and clear. Over 90% of experts rated the statements as important or somewhat important for a graduating senior in biology to understand.ConclusionsThis list provides a foundation for both education researchers and evolution educators. Education researchers who investigate student thinking and who develop research-based measurement tools can use this list to determine key concepts on which to focus their future work. Educators can use this list to guide the development of learning objectives for speciation instruction. Future work should investigate what concepts are reasonable for an undergraduate to master in a 4-year degree.

Moving Evolution Education Forward: A Systematic Analysis of Literature to Identify Gaps in Collective Knowledge for Teaching.

Evolution is a unifying theory in biology and is challenging for undergraduates to learn. An instructor's ability to help students learn is influenced by pedagogical content knowledge (PCK), which is topic-specific knowledge of teaching and learning. Instructors need PCK for every topic they teach, which is a tremendous body of knowledge to develop alone. However, investigations of undergraduate thinking and learning have produced collective PCK that is available in peer-reviewed literature. Currently, it is unclear whether the collective PCK available adequately addresses the topics in evolution that college instructors teach. We systematically examined existing literature to determine what collective PCK for teaching evolution is available and what is missing. We conducted an exhaustive literature search and analyzed 316 relevant papers to determine: the evolutionary topics addressed; whether the focus was student thinking, assessment, instructional strategies, or goals; and the type of work (e.g., empirical, literature review). We compared the collective PCK available in the literature with the topics taught in a sample of 32 undergraduate evolution courses around the country. On the basis of our findings, we propose priorities for the evolution education research community and propose that PCK is a useful lens for guiding future research on teaching and learning biology.

Calanoid copepods in central Chilean and Chilean Patagonian lakes (33-55°S, Chile), probable ecological key role in pelagic environments

The Patagonian lakes (38-55°S) are characterized by their marked oligotrophy, low number of species of crustacean zooplankton, and a marked predominance of calanoid copepods. Within this context, we considered that a review about the ecology of the zooplankton in central and southern Chilean lakes would be useful, aiming to understand the ecological importance of this group. Data obtained from the literature for freshwater bodies in central and southern Chilean lakes were analysed. In addition, data from various bays with widely differing trophic status in Llanquihue Lake were examined. The results revealed the existence of originally pristine and oligotrophic sites, all with a low number of species and marked calanoid dominance. However, in northern Patagonia there are many lakes in which human intervention has caused an increase in phytoplankton activity, with a consequent replacement of calanoid copepods by daphniid cladocerans. Other important factors that could affect the zooplankton community would be fish predation, which is due to generate a decrease in large-bodied groups of zooplankton; and stress due to exposure to natural ultraviolet radiation. Ecological, biogeographical, and evolutionary topics are discussed within the framework described.

Teaching evolution to creationist students: the ultimate challenge

Despite overwhelming evidence for the common ancestry of life and evolution by natural selection, ideas invoking direct creation persist, disrupting teaching evolution as a central biological concept. While originating within fundamentalist Protestantism in the USA, creationist views are now prominent elsewhere and in other religions. Responses by educators include ignoring evolution; excluding evolutionary topics especially provocative to creationist students; advocating evolution while ignoring, disparaging or ridiculing creationism; distinguishing between scientific and religious approaches before considering only the scientific; and acknowledging evolution and creationist positions as different world views that one may understand, but not necessarily accept. Here, we argue that any chance of success in teaching evolution to creationist students requires elements of the last two of these approaches. Applying them requires understanding students' worldviews and the methods and limitations of science, as well as employing learning activities that engage, not alienate. In this context, we describe the creationist positions that may be encountered when teaching evolution, the fundamentals appropriate to teaching scientific method, and the teaching strategies of affirmative neutrality and procedural neutrality that educators may use to counter creationist views when teaching evolution. We regard understanding of the common ancestry of life and natural selection and other evolutionary mechanisms as threshold concepts that, once grasped, can transform students' interpretations of biology and possibly their world views. Mentioning creationism in the context of science education may be a dangerous idea, but what is worse - to establish some common ground with creationist students in the hope of leading them to an understanding of evolution, or to leave them ignorant of any evolutionary concepts at all?

New directions in island biogeography

ABSTRACTAimMuch of our current understanding of ecological and evolutionary processes comes from island research. With the increasing availability of data on distributions and phylogenetic relationships and new analytical approaches to understanding the processes that shape species distributions and interactions, a re‐evaluation of this ever‐interesting topic is timely.LocationIslands globally.MethodsWe start by arguing that the reasons why island research has achieved so much in the past also apply to the future. We then critically assess the current state of island biogeography, focusing on recent changes in emphasis, including research featured in this special issue ofGlobal Ecology and Biogeography. Finally, we suggest promising themes for the future. We cover both ecological and evolutionary topics, although the greater emphasis on island ecology reflects our own backgrounds and interests.ResultsMuch ecological theory has been directly or indirectly influenced by research on island biotas. Currently, island biogeography is renascent, with research focusing on, among other things, patterns and processes underlying species interaction networks, species coexistence and the assembly of island communities through ecological and evolutionary time. Continuing island research should provide additional insight into biological invasions and other impacts of human activities, functional diversity and ecosystem functioning, extinction and diversification, species pools and more. Deeper understanding of the similarities and differences between island and mainland systems will aid transferability of island theory to continental regions.Main conclusionsAs research in biogeography and related fields expands in new directions, islands continue to provide opportunities for developing insights, both as natural laboratories for ecology and evolution and because of the exceptions islands often present to the usual ‘rules’ of ecology. New data collection initiatives are needed on islands world‐wide and should be directed towards filling gaps in our knowledge of within‐island distributions of species, as well as the functional traits and phylogenetic relationships of island species.

Variation in Tupi languages: Genealogy, language change, and typology

At least 40 spoken languages form the large tupi family in its subfamilies tupi-Guarani, Mawe, Aweti, Arikem, Juruna, Monde, tupari, Munduruku, ramarama and Purubora, providing a wealth of data for linguistic studies about variation – variation explained by genetic relations (common origin, ultimately from the presumed language ‘proto-tupi’) or by contact relations with other indigenous or non-indigenous languages. the interest in indigenous languages has increased in recent years, evinced by the publication of a growing number of descriptive, historical-comparative and other studies. Most studies published in this volume originate from a linguistic symposium organized by Wolf dietrich and sebastian drude at the 54th international Congress of Americanists in Vienna, in 2012. the symposium was dedicated to “Historical variation and variation by contact among the tupian languages”. those studies that deal with problems of linguistic genealogy, genetics, language change, and syntactic typology across several tupi languages or a single tupi language are published in this special “dossier”. the first six papers deal with problems of the whole tupi family or at least one of its sub-families. three of them investigate evolutionary topics; three are cross-linguistic synchronic studies. Eduardo dos santos and colleagues from the area of human genetics, in their paper “origins and demographic dynamics of tupi expansion: a genetic tale”, use recent genetic data in order to show that the Madeira-Guapore region may indeed be considered to be the tupi homeland. Ancient tupi expansion within the Madeira-Guapore region and dispersion to other south American areas seems to be related to patrilocal practices. this outcome allows for new interpretations of archaeological and linguistic data, for instance the dispersion of female associated technologies like ceramics and terminologies related to ceramics. Ana Vilacy Galucio and colleagues from the tupi Comparative Project, in their paper “on the genetic relationship and degree of relatedness with the tupi linguistic family”, present the first lexicostatistical and phylogenetic attempt of the genetic classification of most languages of the tupi family, including four languages of the tupi-Guarani branch. Based on all relevant previous studies of particular branches of the family, and applying lexicostatistics to a semantically based word list,, the article demonstrates that the two major branches of the state of rondonia, Monde and tupari, have high percentages of shared cognates. this supports the results of the first article of this volume. the paper by sergio Meira and sebastian drude gives an overview of their reconstruction of the segmental phonology of Proto-Maweti-Guarani, the hypothetical proto-language from which modern Mawe, Aweti, and the

Dynamic Online HDP model for discovering evolutionary topics from Chinese social texts

User-generated content such as online reviews in social media evolve rapidly over time. To better understand the social media content, users not only want to examine what the topics are, but also want to discover the topic evolution patterns. In this paper, we propose a Dynamic Online Hierarchical Dirichlet Process model (DOHDP) to discover the evolutionary topics for Chinese social texts. In our DOHDP model, the evolutionary processes of topics are considered as evolutions in two levels, i.e. inter-epoch level and intra-epoch level. In inter-epoch level, the corpus of each epoch is modeled with an online HDP topic model, and the social texts are generated in a sequence mode. In the intra-epoch level, the time dependencies of historical epochs are modeled with an exponential decay function in which more recent epochs have a relatively stronger influence on the model parameters than the earlier epoch. Furthermore, we implement our DOHDP model using a two-phase online variational algorithm. Through comparing our DOHDP model with other related topic models on Chinese social media dataset Tianya-80299, the experiment results show that DOHDP model provides the best performance for discovering the evolutionary topics of Chinese social texts.

A Trailing Paper Trail

A Trailing Paper Trail

‘His father’s voice’: Phonographs and Heredity in the Fiction of Samuel Butler

The article explores the interaction between concepts of heredity and technologies of voice recording and reproduction in the late-Victorian imagination through the example of Samuel Butler. Butler’s writing on evolutionary topics frequently conceptualized heredity as a record of ancestral voices echoing through their descendants. His Lamarckian view of evolution caused him to present heredity as analogous to the phonograph, recording the experiences of individuals, storing them in the germ plasm and reproducing them in the offspring. Theorists of hereditary memory such as Ewald Hering described it as a form of vibration and inscription, emphasizing its parallels with phonography. At the same time, language and the physical voice seemed equally haunted for Butler, resonating with the thoughts, feelings, and urges of past generations. I pursue these themes through a close reading of his posthumously published novel The Way of All Flesh (1903). Butler makes an interesting case study for this subject since his ideas about the inheritance of ancestral voices were inseparable from his complex personal relations with his family. His efforts to escape the influence of his parents were bound up with the notion of escaping the habitual ‘grooves’ in which they lived, thought, and spoke. Such escape sometimes seems impossible in Butler’s vision, with long-term heredity and immediate social convention rendering people echoes of their predecessors. However, the life experience of the individual offered possibilities for breaking with the voices of the past, etching new grooves of habit and redirecting old ones. Further, heredity in Butler’s vision was not a single, commanding voice but a cacophony of competing voices screaming to be heard. In this sense, what seemed like rebellion against the voice of one’s ancestor might turn out to be obedience towards another one. Butler conceived of intellectual influence in the same way, placing thinkers and writers in a pseudo-familial (and perhaps proto-Freudian) relationship with their predecessors. His concern with escaping ancestral voices existed in tension, though, with his desire to render his own voice immortal through his literary work.

Oddball Science: Why Studies of Unusual Evolutionary Phenomena Are Crucial

Concerns about the US budget deficit are pushing government research funding toward utilitarian and translational research at the expense of basic science (Hand et al. 2013). Science funding decisions are increasingly at risk of becoming politicized, and reductions in basic science funding are often justified as eliminating wasteful government spending. Indeed, critics have named several government-funded basic research projects as examples of waste (e.g., Fahrenthold 2013). Recent examples include studies on duck penises, shrimp running on a treadmill, robotic squirrels, and snail sex. The criticized programs are typically studies of organisms with unusual morphologies or behaviors that have no obvious application to society. The appeal of such criticism is obvious; at first glance, studies of odd evolutionary topics seem frivolous, even wasteful, especially in tough economic times and when compared with applied science intended to cure disease, develop renewable energy, or improve agriculture. The temptation to argue that the federal government should fund only science with a foreseeable benefit is understandable, especially because guidelines of the National Science Foundation (NSF) require reporting the economic impacts of government-funded research in all fields. Some biology researchers have even suggested—misguidedly, in our opinion—that their field should address the interface between basic and applied science, with a focus on projects that address an applied challenge (Cooke 2011, Aarssen 2013). Furthermore, Aarssen (2013) argued that “university research—with no particular societal benefit in mind— has largely run its course” (p. 417). The problem with this view is that it assumes that human innovation arises in a logical fashion from planned research. History says otherwise: Innovations often arise from unlikely sources. This phenomenon was recognized last year with the establishment of the Golden Goose Awards for projects that may sound odd but that produce significant—usually unforeseen—health or economic benefits (Underwood 2012). Although seeking out projects that are likely to lead to applications may be a good strategy for securing funding, we maintain that reducing our ability to creatively examine unique biological phenomena will ultimately harm not only education and health but also the ability to innovate— a major driver of the global economy. The study of organisms typically centers on evolutionary innovations—the biological structures and phenomena that enable new functions or behaviors. These adaptations are often surprising and may seem bizarre, but they are the product of over 3 billion years of evolution and are often associated with the successful exploitation of new habitats. Studies of these seemingly oddball adaptations have jumpstarted myriad technological applications. They began, however, as basic scientific questions. Here, we highlight some examples that should be useful for anyone defending funding for basic biological research.

Immersive simulations for smart classrooms: exploring evolutionary concepts in secondary science

This article presents the design of an immersive simulation and inquiry activity for technology-enhanced classrooms. Using a co-design method, researchers worked with a high school biology teacher to create a rainforest simulation, distributed across several large displays in the room to immerse students in the environment. The authors created and evaluated two iterations of a design where students gathered evidence of evolution using networked tablet computers that scaffolded their interactions with peers and with the room itself. Outcomes suggest that the immersive simulation engaged students, helped them to establish and build upon ideas about evolution and promoted learning of challenging biological concepts. Student explanations from the second implementation demonstrated increased variation in ideas about evolutionary topics compared to those in the first iteration. Relevant design features from the two iterations are discussed.

Similar patterns of individual niche use are revealed by different time‐integrated trophic tracers (stable isotopes and parasites)

AbstractTwo unconnected time‐integrated tracers of niche use provided similar conclusions about individual foraging behaviour and niche adaptations (functional traits in head shape) within a subarctic lake population of Arctic charr (Salvelinus alpinus). Zooplanktivorous individuals mainly from the pelagic zone were characterised by having low δ13C values, high infections of the parasites transmitted by pelagic copepods (especially Diphyllobothrium spp.) and slender heads with long snouts. In contrast, fish individuals that had consumed benthic prey in the littoral zone were enriched in δ13C and had high abundances of parasites transmitted by Gammarus lacustris (Cyathocephalus truncatus and Cystidicola farionis) and a robust head shape. There were strong positive correlations between individual δ13C values and the abundance of the two parasite species transmitted by Gammarus, but a negative correlation between δ13C and the infection of copepod‐borne parasites. The close relationships between diet variation (foraging behaviour), the time‐integrated ecological tracers (SI and parasites) and functional trophic morphology (niche adaptations) evidently reflect long‐term temporally stable niche use of each individual predator. The two independent time‐integrated tracers both gave valuable information of specialised trophic behaviour at the individual level, which is an important basis for studies related to ecological (e.g., resource partitioning) and evolutionary (e.g., polymorphism) topics within a population.