How to Win the Evolution War: Teach Macroevolution!

If the American public understood what is actually known about the major evolutionary transitions in the history of life and how we know about them, uncertainty about evolution would drop precipitously, creationist arguments would fall on deaf ears, and public education in biology would make much more sense than it now does. Macroevolution must take a much more prominent place in K-12 science teaching. To do so, a curriculum must be redeveloped at both K-12 and college levels, so that preparation in macroevolution is a required part of K-12 biology preparation.     

Ancon sheep: a now disproven example of macroevolution.

The Ancon breed of sheep provided, for decades, a critical support for the existence of major evolutionary changes or jumps called "sports." Putative examples of sports have been used as evidence of rapid macroevolution since Darwin first discussed the Ancon sheep mutation in 1859. Ancon sheep had very short legs that were considered an advantage for shepherds because the sheep were less likely to escape over fences. Many textbooks and articles implied that the breed was an example of how a major new trait could evolve in a single generation. The Ancon sheep example has been used both to prove gradual Darwinism and also to argue for rapid evolution as opposed to gradualism. It now is recognized that Ancon sheep resulted from genetic diseases, and that they usually suffered from achondroplasia. The so-called new breed had so many major health problems that the condition caused the breed's extinction decades ago, yet was mentioned in textbooks as evidence for evolutionary jumps as recently as 2005.     

Cryptic designs on the peppered moth

In a provocative recent book, Jonathan Wells (2000) decries what he discerns as a systematic pattern in how introductory biology textbooks "blatantly misrepresent" ten routinely cited examples offered as evidence for evolution. Each of these examples, according to Wells, is fraught with interpretive problems and, as such, textbooks that continue to use them should at the very least be accompanied by warning labels. The following essay critiques his reasoning with reference to one of these examples, the phenomenon of industrial melanism. After criticizing Wells's specific argument, the essay draws several conclusions about the nature of science lost in his account.     

PHYLOGENIES WITHOUT FOSSILS

Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.     

Examining the Interaction of Acceptance and Understanding: How Does the Relationship Change with a Focus on Macroevolution?

The goal of this research was to illuminate the relationship between students’ acceptance and understanding of macroevolution. Our research questions were: (1) Is there a relationship between knowledge of macroevolution and acceptance of the theory of evolution?; (2) Is there a relationship between the amount of college level biology course work and acceptance of evolutionary theory and knowledge of macroevolution?; and (3) Can college student acceptance of the theory of evolution and knowledge of macroevolution change over the course of a semester? The research participants included 667 students from a first-semester biology course and 74 students from the evolutionary biology course. Data were collected using both the MATE (a measure of the acceptance of evolutionary theory) and the MUM (a measure of understanding of macroevolution). Pre-instruction data were obtained for the introductory biology course, and pre- and post-data were obtained for the evolutionary biology course. Analysis revealed acceptance of evolution (as measured by the MATE) was correlated to understanding of macroevolution, and the number of biology courses was significantly correlated to acceptance and knowledge of macroevolution. Finally, there was a statistically significant change in students’ understanding of macroevolution and acceptance of evolution after the one-semester evolutionary biology course. Significance of these findings is discussed.     

Tree thinking for all biology: the problem with reading phylogenies as ladders of progress

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved "tree thinking" is crucial. The most-serious problem comes from reading trees as ladders from "left to right"--many biologists assume that species-poor lineages that appear "early branching" or "basal" are ancestral--we call this the "primitive lineage fallacy". This mistake causes misleading inferences about changes in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21(st) century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19(th) century notions about the ladder of progress driving evolution.     

In response to an open invitation for comments on AAAS project 2061's Benchmark books on science. Part 1: documentation of serious errors in cell biology

Project 2061 was founded by the American Association for the Advancement of Science (AAAS) to improve secondary school science education. An in-depth study of ten 9 to 12th grade biology textbooks led to the verdict that none conveyed "Big Ideas" that would give coherence and meaning to the profusion of lavishly illustrated isolated details. However, neither the Project report itself nor the Benchmark books put out earlier by the Project carries what deserves the designation of "Big Ideas." Worse, in the two earliest-published Benchmark books, the basic unit of all life forms--the living cell--is described as a soup enclosed by a cell membrane, that determines what can enter or leave the cell. This is astonishing since extensive experimental evidence has unequivocally disproved this idea 60 years ago. A "new" version of the membrane theory brought in to replace the discredited (sieve) version is the pump model--currently taught as established truth in all high-school and college biology textbooks--was also unequivocally disproved 40 years ago. This comment is written partly in response to Bechmark's gracious open invitation for ideas to improve the books and through them, to improve US secondary school science education.     

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.     

Transforming Our Thinking about Transitional Forms

A common misconception of evolutionary biology is that it involves a search for “missing links” in the history of life. Relying on this misconception, antievolutionists present the supposed absence of transitional forms from the fossil record as evidence against evolution. Students of biology need to understand that evolution is a branching process, paleontologists do not expect to find “missing links,” and evolutionary research uses independent lines of evidence to test hypotheses and make conclusions about the history of life. Teachers can facilitate such learning by incorporating cladistics and tree-thinking into the curriculum and using evograms to focus on important evolutionary transitions.     

Time-dependent speciation and extinction from phylogenies: a least squares approach

Molecular phylogenies contribute to the study of the patterns and processes of macroevolution even though past events (fossils) are not recorded in these data. In this article, I consider the general time-dependent birth-death model to fit any model of temporal variation in speciation and extinction to phylogenies. I establish formulae to compute the expected cumulative distribution function of branching times for any model, and, building on previous published works, I derive maximum likelihood estimators. Some limitations of the likelihood approach are described, and a fitting procedure based on least squares is developed that alleviates the shortcomings of maximum likelihood in the present context. Parametric and nonparametric bootstrap procedures are developed to assess uncertainty in the parameter estimates, the latter version giving narrower confidence intervals and being faster to compute. I also present several general algorithms of tree simulation in continuous time. I illustrate the application of this approach with the analysis of simulated datasets, and two published phylogenies of primates (Catarrhinae) and lizards (Agamidae).     

On the origin and evolution of major morphological characters

Although the mathematical principles underpinning population-level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least-constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained ("burdened", in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever-increasing restriction on the scope of evolution, nor does it require drastic events to overcome or "break" it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype-phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make-up being of secondary importance. It should prove possible to recast traditional notions of body-plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.     

Evolutionists and creationists at the dinner table

The evolutionist and creationist debate about human origins has contested the content of textbooks, what is taught in classrooms, and what is discussed on the Internet. The controversy has spawned public‐interest groups that continue to frame the debate. The National Center for Science Education monitors attempts to incorporate creationism into the classroom and textbooks. The Institute for Creation Research and the Discovery Institute have invested heavily in pushing for changes in the curriculum by teaching creationism as an alternative to evolution. While this dispute usually focuses on the reality of the fossil evidence for human evolution, a less formal battle is now being waged at the proverbial dinner table.     

Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages

Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.     

MicroRNAs and the Operon paper

The “Operon paper” by F. Jacob and J. Monod started 50 years of research into understanding how the expression of genes is regulated on a molecular level. Ten years ago, microRNAs (miRNAs) emerged as major regulators of eukaryotic gene expression. Here, I will review the basic principles of gene regulation by miRNAs and how these principles can be linked to insights from the Operon paper. A lot of what is understood about miRNAs required a combination of computational and experimental methods. I will discuss some examples that illustrate the power of this approach.     

Prebiotic world, macroevolution, and Darwin’s theory: a new insight

Darwin’s main contribution to modern biology was to make clear that all history of life on earth is dominated by a simple principle, which is usually summarised as 'descent with modification'. However, interpretations about how this modification is produced have been controversial. In light of the data provided by recent studies on molecular biology, developmental biology, genomics, and other biological disciplines we discuss, in this paper, how Darwin's theory may apply to two main 'types' of evolution: that occurring in the prebiotic world and that regarding the acquisition of major key-innovations differentiating higher-taxa, which makes up part of the so-called macroevolution. We argue that these studies show that evolution is a fascinating, complex and multifaceted process, with different mechanisms drivin it on different occasions and in different places.     

The origin of angiosperms: New and old problems

Recent palaeobotanical discoveries assisted by the thorough morphological analysis of 'living fossils'-archaic extant plants-have brought to light many unexpected features of the early angiosperms and their immediate precursors, while studies in palaeoecology have provided a basis for deciphering the chronology of evolutionary events and their environmental forcing. Our previous ideas of what is primitive and what angiosperm ancestors looked like are presently under revision. We now have a clearer picture of how macroevolution proceeds and how a large taxon could come into being.     

An exploration of instructor perceptions of community college students’ attitudes towards evolution

Background

Faculty perception of student knowledge and acceptance of subject matter affects the choice of what to teach and how to teach it. Accurate assessment of student acceptance of evolution, then, is relevant to how the subject should be taught. To explore the accuracy of such assessment, we compared how community college instructors of life sciences courses perceive students’ attitudes towards evolution with those students’ actual attitudes towards evolution.

Results

The research had two components: (1) a survey of students of several biology classes at a community college about their acceptance of evolutionary theory and (2) interviews with the biology faculty teaching those classes about their perceptions of their students’ attitudes towards evolution. Results of the study indicate relatively high levels of acceptance of evolution among community college students at this West Coast institution. We also found that community college instructors of life sciences courses varied in accuracy of their perceptions of their students’ attitudes towards evolution–but not systematically. Although one professor assessed each class quite accurately, the other two professors frequently underestimated the acceptance of evolution among their students.

Conclusions

Errors in perception seemed independent of whether the class was composed of majors, nonmajors, or a combination. Clearly, in our sample there is much idiosyncrasy regarding community college instructor accuracy concerning student opinions about evolution.

     

我国高校遗传学教材的出版与使用现状的调查

利用国家图书馆“文津”搜索系统发现, 我国自恢复高考以来, 累计出版遗传学教材895部, 其中理论教材588部(65.7%)、实验教材122部(13.6%)、教学参考资料185部(20.7%)。这些教材中, 医学遗传学最多, 普通遗传学其次, 动植物微生物遗传学较少。对教材的名称、第一编(著)者和出版机构的分析发现, 名称为“医学遗传学”的教材有91部, 左伋教授编写了9部教材, 是编写教材最多的“第一编(著)者”, 科学出版社共出版了179部(占20%)教材, 是遗传学教材出版的主力军。利用问卷调查发现, 戴灼华等主编的《遗传学》(第二版)是目前使用最广泛的理论教材, 实验教材则多用自编讲义或教材。文章也对教材中存在的问题, 如更新周期长、配套落后、同名严重、遗传学故事写得太少、特色插图凤毛麟角、印刷页字数过满等进行了剖析, 并提出了解决途径。     

A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics

The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available databases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea + Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida + Euchelicerata). "Crustacea" is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a Hexapod-Branchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies.     

Ecophylogenetics: advances and perspectives

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.