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

Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage

Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.

Reticulate evolution of the tertiary relict Osmanthus

When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.

New Earwigs from the Middle Jurassic Jiulongshan Formation of Northeastern China (Dermaptera)

Two new genera and species of Dermaptera are described from the Middle Jurassic Jiulongshan Formation of Daohugou, Inner Mongolia, China: Applanatiforceps angustus gen. et sp. nov. in the archidermapteran family Protodiplatyidae, and Ekpagloderma gracilentum gen et sp. nov. in the eodermapteran family Semenoviolidae. Applanatiforceps shares the typical characters of the extinct suborder Archidermaptera (e.g., pentamerous meta tarsi, filiform and multimerous cerci) and externalized ovipositor. The family identity of the Protodiplatyidae can be further distinguished by comparing this new genus with other genera of the Protodiplatyidae. As a result of its large compound eyes, tegmina without venation, body sparsely setose, legs rather short and slender, and shape of the veinless tegmina, Ekpagloderma is classified in the subfamily Aglyptodermatinae. Ekpagloderma not only has the typical features of the Aglyptodermatinae, but also exhibits a more primitive slender segmented cerci, which is different from all other genera of Eodermaptera. In fact, the diversity of Eodermaptera as known today indicates some of the challenges in understanding the suborder and whether or not it is monophyletic as historically construed, or if the separation of Turanodermaptera is justified.

Octavio Ocampo, Mexican painter: a metamorphic look at the discourse between the local and the global

Art and science is an area of research that has strengthened recently, mainly due to the impact of interdisciplinary work. At the same time, approaches between the humanities and the sciences have succeeded in re-signifying traditional views towards critical positions such as postcolonialism, especially in the colonially so-called "Global South". In this paper, we want to review the case of the work of the Mexican artist Octavio Ocampo through works that present the case of biological and cultural evolution. From this, we want to reflect on the public perception of science in Mexico, the tensions between social and natural sciences, and the urgent need to strengthen the postcolonial discourse in scientific practice.

Mapping species diversification metrics in macroecology: Prospects and challenges

The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.

The Core Concepts, Competencies and Grand Challenges of Comparative Vertebrate Anatomy and Morphology

Core concepts offer coherence to the discourse of a scientific discipline and facilitate teaching by identifying large unifying themes that can be tailored to the level of the class and expertise of the instructor. This approach to teaching has been shown to encourage deeper learning that can be integrated across subdisciplines of biology and has been adopted by several other biology subdisciplines. However, Comparative Vertebrate Anatomy, although one of the oldest biological areas of study, has not had its core concepts identified. Here, we present five core concepts and seven competencies (skills) for Comparative Vertebrate Anatomy that came out of an iterative process of engagement with the broader community of vertebrate morphologists over a 3-year period. The core concepts are (A) evolution, (B) structure and function, (C) morphological development, (D) integration, and (E) human anatomy is the result of vertebrate evolution. The core competencies students should gain from the study of comparative vertebrate anatomy are (F) tree thinking, (G) observation, (H) dissection of specimens, (I) depiction of anatomy, (J) appreciation of the importance of natural history collections, (K) science communication, and (L) data integration. We offer a succinct description of each core concept and competency, examples of learning outcomes that could be used to assess teaching effectiveness, and examples of relevant resources for both instructors and students. Additionally, we pose a grand challenge to the community, arguing that the field of Comparative Vertebrate Anatomy needs to acknowledge racism, androcentrism, homophobia, genocide, slavery, and other influences in its history and address their lingering effects in order to move forward as a thriving discipline that is inclusive of all students and scientists and continues to generate unbiased knowledge for the betterment of humanity. Despite the rigorous process used to compile these core concepts and competencies, we anticipate that they will serve as a framework for an ongoing conversation that ensures Comparative Vertebrate Anatomy remains a relevant field in discovery, innovation, and training of future generations of scientists.

Developing the BETTSI: A tree-thinking diagnostic tool to assess individual elements of representational competence

Phylogenies are a ubiquitous visual representation of core concepts in evolutionary biology and it is important that students develop an ability to read and correctly interpret these diagrams. However, as with any representation of complex disciplinary information, learning to correctly interpret phylogenies can be challenging, requiring that a diversity of educational strategies be deployed. Representational competence is the ability to develop and effectively use abstract representations. Accurately interpreting a phylogenetic tree as a presentation of evolutionary relationships requires that students develop general representational competence as well as knowledge of specific technical aspects of tree interpretation, such as knowing the graphical components of trees and what they represent. Here, we report on the development of a basic diagnostic tool of students' representational competence and technical skills with phylogenies, the Basic Evolutionary Tree-Thinking Skills Instrument (BETTSI). This short, multiple-choice instrument was designed to provide instructors with a quick diagnostic of students' ability to read and interpret phylogenies. It has been checked for reliability and validity and provides a convenient formative and summative assessment of students' understanding of evolutionary trees.

A comparison study of human examples vs. non-human examples in an evolution lesson leads to differential impacts on student learning experiences in an introductory biology course

Background

Instructors can teach evolution using any number of species contexts. However, not all species contexts are equal, and taxa choice can alter both cognitive and affective elements of learning. This is particularly true when teaching evolution using human examples, a promising method for evolution instruction that nevertheless comes with unique challenges. In this study, we tested how an evolution lesson focused on a human example may impact students’ engagement, perceived content relevance, learning gains, and level of discomfort, when compared to the same lesson using a non-human mammal example. We use this isomorphic lesson and a pre-post study design administered in a split-section introductory biology classroom to isolate the importance of the species context.

Results

For two of the four measurements of interest, the effect of using human examples could not be understood without accounting for student background. For learning gains, students with greater pre-class content knowledge benefited more from the human examples, while those with low levels of knowledge benefited from the non-human example. For perceived relevance, students who were more accepting of human evolution indicated greater content relevance from the human example. Regardless of condition, students with lower evolution acceptance reported greater levels of discomfort with the lesson.

Conclusions

Our results illustrate the complexities of using human examples to teach evolution. While these examples were beneficial for many students, they resulted in worse outcomes for students that were less accepting of evolution and those who entered the course with less content knowledge. These findings demonstrate the need to consider diverse student backgrounds when establishing best practices for using human examples to teach evolution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12052-021-00148-w.

Modeling and Measuring Tree-Reading Skills in Undergraduate and Graduate Students

Evolutionary trees are central to learning about evolutionary processes, yet students at all educational levels struggle to read and interpret them. The synthetic tree-reading model (STREAM), based on published and not yet empirically tested models, was tested to determine whether the assumed hierarchy of the model could be substantiated and how far students' skills could be distinguished empirically. We developed a tree-reading test instrument based on STREAM and assessed it with 592 undergraduate and graduate biology students. Following item response theory, we conducted a dimensional analysis and evaluated item difficulty. Investigating item difficulty and the resulting Wright map showed that skill levels displayed a broad scatter of overlapping item difficulty. Furthermore, the skill level assumed easiest was actually the third most difficult. No conclusive evidence of the hierarchical nature of the model was obtained. Dimensional analysis showed that a five-dimensional model outperformed all other reasonable models, corroborating that the skills could be arranged in empirically differentiable groups. Consequently, we revised the STREAM by discarding the hierarchical organization, using a five-dimensional organization instead. Comparison of the revised STREAM with another recently published approach showed that, although these two instruments have a different focus, they are supplemental approaches that show comparable results.

Seeing the Woods for the Trees Again: Analyzing Evolutionary Diagrams in German and US University-Level Textbooks

Phylogenetic trees are important tools for teaching and understanding evolution, yet students struggle to read and interpret them correctly. In this study, we extend a study conducted by Catley and Novick (2008) by investigating depictions of evolutionary trees in US textbooks. We investigated 1197 diagrams from 11 German and 11 United States university textbooks, conducting a cross-country comparison and comparing the results with data from the 2008 study. A coding manual was developed based on the 2008 study, with extensions focused on additional important aspects of evolutionary trees. The US and German books showed only a low number of significant differences, typically with very small impacts. In both samples, some characteristics that can render reading trees more difficult or foster misconceptions were found to be prevalent in various portions of the diagrams. Furthermore, US textbooks showed fewer problematic properties in our sample than in the 2008 sample. We conclude that evolutionary trees in US and German textbooks are represented comparably and that depictions in US textbooks have improved over the past 12 years. As students are confronted with comparable depictions of evolutionary relatedness, we argue that findings and materials from one country should easily be transferable to the other.

Bryophytes are not early diverging land plants

Phylogenetic trees have permeated biology. However, an understanding of how to interpret phylogenies has lagged behind, notably in publications outside of evolutionary biology. Here I argue that some language commonly used in plant systematics has contributed to the confusion by describing phylogenetic trees using intuitive but misleading terms reminiscent of Aristotle's Scala Naturae. These terms (perhaps inadvertently) misrepresent evolution, not as a process acting on all living species, but rather as a progression of successively diverging lineages leading to a group that represents a subjectively defined endpoint. My goal here is to show how thinking of the tree of life in terms of early-diverging lineages and higher groups can distort evolutionary literacy, confound interdisciplinary communication, and potentially bias research agendas. I focus on the relationship between bryophytes and angiosperms as a case study, but the theme applies to all branches of the tree of life. Fortunately, evolutionary biologists have developed an easily understood alternative framework - tree thinking - which I highlight as a means to promote a clear understanding of phylogenies across sub-disciplines of biology, and between practicing biologists and students, or members the public which funds much of our work.

Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.

Ontogenetic development of the shoulder joint muscles in frogs (Amphibia: Anura) assessed by digital dissection with implications for interspecific muscle homologies and nomenclature

Previous myological studies show inconsistencies with regard to the identification and naming of the shoulder joint muscles in frogs and toads (Amphibia: Anura). Those inconsistencies were revealed and resolved by assessing the ontogenetic development, innervation, and adult morphology of selected anuran species representing ancient lineages and two major neobatrachian groups. To do so, digital dissections of volumes acquired by histological serial sectioning, episcopic microtomy, and contrast-enhanced micro-computed tomography scanning were performed and three-dimensional reconstructions were derived. Muscle units crossing the shoulder joint were defined, their ontogenetic development was described, their homology across species was established, and a consistent nomenclature was suggested. The mm. anconaeus, dorsalis scapulae, latissimus dorsi, and the group of scapulohumeralis muscles were ontogenetically derived from the dorsal pre-muscle mass present in all tetrapods. The ventral pre-muscle mass gave rise to the mm. cleidohumeralis, episternohumeralis, supracoracoideus, coracoradialis, subcoracoscapularis, coracobrachialis, and pectoralis. The results indicate that the mm. anconaeus, dorsalis scapulae, latissimus dorsi, coracoradialis, and the portionis sternalis and abdominalis of the m. pectoralis have consistently been recognized and denoted in previous studies, whereas the names for the muscle units commonly denoted as m. coraco-brachialis longus and as parts of the m. deltoideus are misleading with regard to the ontogenetic origin of these muscles. The mm. scapulohumeralis profundus anterior and posterior, although present, have been overlooked in some studies. The mm. cleidohumeralis, supracoracoideus, and coracobrachialis are present with two parts or portions in some species, these portions have previously not always been recognized and assigned correctly.

On the evolution and development of morphological complexity: A view from gene regulatory networks

How does morphological complexity evolve? This study suggests that the likelihood of mutations increasing phenotypic complexity becomes smaller when the phenotype itself is complex. In addition, the complexity of the genotype-phenotype map (GPM) also increases with the phenotypic complexity. We show that complex GPMs and the above mutational asymmetry are inevitable consequences of how genes need to be wired in order to build complex and robust phenotypes during development. We randomly wired genes and cell behaviors into networks in EmbryoMaker. EmbryoMaker is a mathematical model of development that can simulate any gene network, all animal cell behaviors (division, adhesion, apoptosis, etc.), cell signaling, cell and tissues biophysics, and the regulation of those behaviors by gene products. Through EmbryoMaker we simulated how each random network regulates development and the resulting morphology (i.e. a specific distribution of cells and gene expression in 3D). This way we obtained a zoo of possible 3D morphologies. Real gene networks are not random, but a random search allows a relatively unbiased exploration of what is needed to develop complex robust morphologies. Compared to the networks leading to simple morphologies, the networks leading to complex morphologies have the following in common: 1) They are rarer; 2) They need to be finely tuned; 3) Mutations in them tend to decrease morphological complexity; 4) They are less robust to noise; and 5) They have more complex GPMs. These results imply that, when complexity evolves, it does so at a progressively decreasing rate over generations. This is because as morphological complexity increases, the likelihood of mutations increasing complexity decreases, morphologies become less robust to noise, and the GPM becomes more complex. We find some properties in common, but also some important differences, with non-developmental GPM models (e.g. RNA, protein and gene networks in single cells).

The evolution of feeding within Euchelicerata: data from the fossil groups Eurypterida and Trigonotarbida illustrate possible evolutionary pathways

When the evolution of Euarthropoda is discussed, often the lineage of Chelicerata s. str. is assumed to be the more ‘primitive’ or ‘basal’ part of the tree, especially when compared to the other major lineage, Mandibulata. This claimed primitiveness is (at least partly) based on the assumption that different morphological structures are still in an ancestral state and did not evolve any further. One of these sets of structures is the feeding apparatus, which has been stated to be highly advanced in Mandibulata, but not ‘properly’ developed, or at least not to such a high degree, within Chelicerata s. str. In this study, I reinvestigate the feeding apparatus of different ingroups of Euchelicerata, with a focus on assumed ‘primitive’ groups such as Eurypterida and Trigonotarbida. The basis of this study is a large amount of material from different museum collections, with fossils with the entire feeding apparatuses being exceptionally well preserved. Based on high-resolution micro-photography and three-dimensional imaging, it is possible to resolve fine details of the feeding apparatuses. The results make clear that the feeding apparatuses of different ingroups of Euchelicerata are highly specialised and often possess morphological structures comparable to those of the feeding apparatuses of representatives of Mandibulata, apparently convergently evolved. Though the reconstruction of the evolution of the feeding apparatus within Euchelicerata is to a certain degree hampered by unclear phylogenetic relationships, there was clearly a shortening of the feeding apparatus from posterior (i.e. only the anterior appendages being involved in the feeding apparatus), probably linked to the colonisation of land in Arachnida.

Progress towards the Tree of Eukaryotes

Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or 'supergroups'. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.

Exploratory Activities for Understanding Evolutionary Relationships Depicted by Phylogenetic Trees: United but Diverse

Evolution explains both the unity and the diversity of all organisms, and developing students' ability to represent and communicate evolutionary relationships is an important component of a complete biology education. We present a series of student-centered, exploratory activities to help students develop their tree-thinking skills. In these activities, students use complementary phenotypic and molecular data to explore how to build phylogenetic trees and interpret the evolutionary relationships they represent. This learning module is designed to engage students in the process of science, provide them with active learning experiences using online bioinformatics tools, and foster their appreciation for the evolutionary connections across the tree of life.

Development of an Evolutionary Tree Concept Inventory

Despite the importance of tree-thinking and evolutionary trees to biology, no appropriately developed concept inventory exists to measure student understanding of these important concepts. To address this need, we developed a multiple-choice concept inventory consisting of 24 pairs of items, and we provide evidence to support its use among undergraduate students. A set of learning outcomes was developed to guide the creation of the concept inventory. The learning outcomes, student interviews, and student responses were used to develop and revise inventory items. Supporting evidence was gathered from traditional item analysis, exploratory factor analysis, confirmatory factor analysis, traditional reliability analyses, and comparisons to alternative assessments. Appropriate implementation and utility of the concept inventory are discussed.

Re-thinking the social ladder approach for elucidating the evolution and molecular basis of insect societies

The evolution of large insect societies is a major evolutionary transition that occurred in the long-extinct ancestors of termites, ants, corbiculate bees, and vespid wasps. Researchers have long used 'social ladder thinking': assuming progressive stepwise phenotypic evolution and asserting that extant species with simple societies (e.g. some halictid bees) represent the ancestors of species with complex societies, and thus provide insight into general early steps of eusocial evolution. We discuss how this is inconsistent with data and modern evolutionary 'tree thinking'. Phylogenetic comparative methods with broad sampling provide the best means to make rigorous inferences about ancestral traits and evolutionary transitions that occurred within each lineage, and to determine whether consistent phenotypic and genomic changes occurred across independent lineages.

Analyzing the phylogeny of poplars based on molecular data

Methods for constructing trees using DNA sequences, known as molecular phylogenetics, have been applied to analyses of phylogenetic origin, evolutionary relatedness and taxonomic classification. Combining data sequenced in this study and downloaded from GenBank, we sampled 112 (chloroplast data) / 122 (ITS data) specimens belonging to 49 (chloroplast data) / 46 (ITS data) poplar species or hybrids from six (chloroplast data) / five sections (ITS data). Maximum parsimony and Bayesian inference were used to analyze phylogenetic relationships within the genus Populus based on eight chloroplast combinations and ITS regions. The results suggested that Bayesian inference might be more suitable for the phylogenetic reconstruction of Populus. All Populus species could be divided into two clades: clade 1, including subclades 1 and 2, and clade 2, including subclades 3 and 4. Species within clade 1, involving five sections except for Leuce, clustered coinciding with their two specific main geographical distribution areas: China (subclade 1) and North America (subclade 2). Clustering in subclade 3, section Leuce was confirmed to be of monophyletic origin and independent evolution. Its two subsections, namely Albidae and Trepidae, could be separated by chloroplast data but had frequent gene flow based on ITS data. Phylogeny analysis based on chloroplast data demonstrated once more that section Aigeiros was paraphyletic and further showed that the P. deltoides lineage is restricted in subclade 2 and that P. nigra lineage, located in subclade 3, originated from a hybrid of which an Albidae ancestor species was the material parent. Similarly, section Tacamahaca was found to be paraphyletic and had two lineages: a clade 1 lineage, such as P. cathayana, and a clade 2 lineage, such as P. simonii. Section Leucoides was paraphyletic and closely linked to section Tacamahaca. Their section boundaries were not conclusively delimitated by sequencing information.

Rethinking Living Fossils

Biologists would be mistaken if they relegated living fossils to paleontological inquiry or assumed that the concept is dead. It is now used to describe entities ranging from viruses to higher taxa, despite recent warnings of misleading inferences. Current work on character evolution illustrates how analyzing living fossils and stasis in terms of parts (characters) and wholes (e.g., organisms and lineages) advances our understanding of prolonged stasis at many hierarchical levels. Instead of viewing the concept's task as categorizing living fossils, we show how its primary role is to mark out what is in need of explanation, accounting for the persistence of both molecular and morphological traits. Rethinking different conceptions of living fossils as specific hypotheses reveals novel avenues for research that integrate phylogenetics, ecological and evolutionary modeling, and evo-devo to produce a more unified theoretical outlook.

Seed plant features, distribution patterns, diversity hotspots, and conservation gaps in Xinjiang, China

The flora in Xinjiang is unique. Decisions about biodiversity conservation and management based on seed plant diversity hotspots and conservation gaps in Xinjiang are essential to maintain this unique flora. Based on a species distribution dataset of seed plants, we measured seed plant diversity using species richness and phylogenetic diversity indices. Five percent of Xinjiang’s total land area with the highest biodiversity was used to identify hotspots for each index. In total, eight hotspots were identified. Most hotspots were located in mountainous areas, mainly in the Tianshan Mountains and Altai Mountains. Furthermore, we detected conservation gaps for Xinjiang’s seed flora hotspots by overlaying nature reserve maps on to maps of identified hotspots and we designated priority conservation gaps for hotspots by overlaying global biodiversity hotspot maps on to hotspot conservation gaps maps. Most of Xinjiang’s seed plant hotspots are poorly protected; only 10.45% of these hotspots were covered by nature reserves. We suggest that it is essential to promote network function of nature reserves within these hotspots in Xinjiang to conserve this unique flora.

Further Effects of Phylogenetic Tree Style on Student Comprehension in an Introductory Biology Course

Phylogenetic trees have become increasingly important across the life sciences, and as a result, learning to interpret and reason from these diagrams is now an essential component of biology education. Unfortunately, students often struggle to understand phylogenetic trees. Style (i.e., diagonal or bracket) is one factor that has been observed to impact how students interpret phylogenetic trees, and one goal of this research was to investigate these style effects across an introductory biology course. In addition, we investigated the impact of instruction that integrated diagonal and bracket phylogenetic trees equally. Before instruction, students were significantly more accurate with the bracket style for a variety of interpretation and construction tasks. After instruction, however, students were significantly more accurate only for construction tasks and interpretations involving taxa relatedness when using the bracket style. Thus, instruction that used both styles equally mitigated some, but not all, style effects. These results inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

How and Why to Build a Unified Tree of Life

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study

Two different adaptive immune systems (AIS) are present in the two phyla of vertebrates (jawed vertebrates and cyclostomes). The jawed vertebrate system is based on IG/TCR/RAG/MHC while the cyclostome system is based on VLRCs and AID-like enzymes both systems using homologous Cell types (B-cell and B-cell Like, T-cell and T-cell like). We will present our current view of the evolution of these two AISs and present alternative hypotheses that could explain the apparent convergent evolution of the two systems. We will also discuss why comparative immunology analyses should be based on evolutionary biology approaches and not on the scale of progress one.

Energy Homeostasis in Monotremes

In 1803, the French anatomist Étienne Geoffroy Saint-Hilaire decided that the newly described echidna and platypus should be placed in a separate order, the monotremes, intermediate between reptiles and mammals. The first physiological observations showed monotremes had low body temperatures and metabolic rates, and the consensus was that they were at a stage of physiological development intermediate between "higher mammals" and "lower vertebrates." Subsequent studies demonstrated that platypuses and echidnas are capable of close thermoregulation in the cold although less so under hot conditions. Because the short-beaked echidna Tachyglossus aculeatus, may show very large daily variations in body temperature, as well as seasonal hibernation, it has been suggested that it may provide a useful model of protoendotherm physiology. Such analysis is complicated by the very significant differences in thermal relations between echidnas from different climates. In all areas female echidnas regulate Tb within 1°C during egg incubation. The lactation period is considered to be the most energetically expensive time for most female mammals but lactating echidnas showed no measurable difference in field metabolic rate from non-lactating females, while the lactation period is more than 200 days for Kangaroo Island echidnas but only 150 days in Tasmania. In areas with mild winters echidnas show reduced activity and shallow torpor in autumn and early winter, but in areas with cold winters echidnas enter true hibernation with Tb falling as low as 4.5°C. Monotremes do not possess brown adipose tissue and maximum rates of rewarming from hibernation in echidnas were only half those of marmots of the same mass. Although echidnas show very large seasonal variations in fat stores associated with hibernation there is no relationship between plasma leptin and adiposity. Leptin levels are lowest during post-reproductive fattening, supporting suggestions that in evolutionary terms the anorectic effects of leptin preceded the adiposity signal. BMR of platypuses is twice that of echidnas although maximum metabolism is similar. High levels of thyroid hormones in platypuses may be driving metabolism limited by low body temperature. Monotremes show a mosaic of plesiomorphic and derived features but can still inform our understanding of the evolution of endothermy.

Comparative Auditory Neuroscience: Understanding the Evolution and Function of Ears

Comparative auditory studies make it possible both to understand the origins of modern ears and the factors underlying the similarities and differences in their performance. After all lineages of land vertebrates had independently evolved tympanic middle ears in the early Mesozoic era, the subsequent tens of millions of years led to the hearing organ of lizards, birds, and mammals becoming larger and their upper frequency limits higher. In extant species, lizard papillae remained relatively small (<2 mm), but avian papillae attained a maximum length of 11 mm, with the highest frequencies in both groups near 12 kHz. Hearing-organ sizes in modern mammals vary more than tenfold, up to >70 mm (made possible by coiling), as do their upper frequency limits (from 12 to >200 kHz). The auditory organs of the three amniote groups differ characteristically in their cellular structure, but their hearing sensitivity and frequency selectivity within their respective hearing ranges hardly differ. In the immediate primate ancestors of humans, the cochlea became larger and lowered its upper frequency limit. Modern humans show an unusual trend in frequency selectivity as a function of frequency. It is conceivable that the frequency selectivity patterns in humans were influenced in their evolution by the development of speech.

The Birth of Animal Development: Multicellularity and the Germline

The evolution of multicellular animals has been attributed to many kinds of selective advantage; here I suggest that the evolution of somatic cells to feed and protect the germline was central to the appearance of animals. This would have been driven by selection for extreme anisogamy--the evolution of sperm and egg. Evidence is adduced from the germline stem cells of simple animals (defining germline as any cell that normally produces the next generation via the sexual process) and from the control circuitry ubiquitous in animal germlines. With the soma and its elaboration came animal development, as we understand it.

Incorporating tree-thinking and evolutionary time scale into developmental biology

Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.

Cognitive phylogenies, the Darwinian logic of descent, and the inadequacy of cladistic thinking

There has been a reappraisal of phylogenetic issues in cognitive science, as reconstructing cognitive phylogenies has been considered a key for unveiling the cognitive novelties that set the stage for what makes humans special. In our opinion, the studies made until now have approached cognitive phylogenies in a non-optimal way, and we wish to both highlight their problems, drawing on recent considerations in philosophy of biology. The inadequacy of current visions on cognitive phylogenies stems from the influence of the traditional “linear cladograms,” according to which every seemingly new or more sophisticated feature of a cognitive mechanism, viewed as a novelty, is represented as a node on top of the old and shared elements. We claim that this kind of cladograms does not succeed in depicting the complexity with which traits are distributed across species and, furthermore, that the labels of the nodes of these traditional representational systems fail to capture the “tinkering” nature of evolution. We argue that if we are to conceive of cognitive mechanisms in a multi-dimensional, bottom-up perspective, in accordance with the Darwinian logic of descent, we should rather focus on decomposing these mechanisms into lower-level, generic functions, which have the additional advantage of being implementable in neural matter, which ultimately produces cognition. Doing so renders current constructions of cognitive phylogenies otiose.

Phylogenetic analysis of HpnP reveals the origin of 2-methylhopanoid production in Alphaproteobacteria

Hopanoids are bacterial steroid-like lipids that can be preserved in the rock record on billion-year timescales. 2-Methylhopanoids are of particular interest to geobiologists because methylation is one of the few chemical modifications that remain after diagenesis and catagenesis. 2-Methylhopanes, the molecular fossils of 2-methylhopanoids, are episodically enriched in the rock record, but we do not have a robust interpretation for their abundance patterns. Here, we exploit the evolutionary record found in molecular sequences from extant organisms to reconstruct the biosynthetic history of 2-methylhopanoids using the C-2 hopanoid methylase, HpnP. Based on HpnP phylogenetic analysis, we find that 2-methylhopanoids originated in a subset of the Alphaproteobacteria. This conclusion is statistically robust and reproducible in multiple trials varying the outgroup, trimming stringency, and ingroup dataset used to infer the evolution of this protein family. The capacity for 2-methylhopanoid production was likely horizontally transferred from the Alphaproteobacteria into the Cyanobacteria after the Cyanobacteria's major divergences. Together, these results suggest that the ancestral function of 2-methylhopanoids was not related to oxygenic photosynthesis but instead to a trait already present in the Alphaproteobacteria. Moreover, given that early 2-methylhopane deposits could have been made solely by Alphaproteobacteria before the acquisition of hpnP by Cyanobacteria, and that the Alphaproteobacteria are thought to be ancestrally aerobic, we infer that 2-methylhopanoids likely arose after the oxygenation of the atmosphere. This finding is consistent with the geologic record-the oldest syngenetic 2-methylhopanes occur after the rise of oxygen, in middle Proterozoic strata of the Barney Creek Formation.

Is evolutionary biology becoming too politically correct? A reflection on the scala naturae, phylogenetically basal clades, anatomically plesiomorphic taxa, and 'lower' animals

The notion of scala naturae dates back to thinkers such as Aristotle, who placed plants below animals and ranked the latter along a graded scale of complexity from 'lower' to 'higher' animals, such as humans. In the last decades, evolutionary biologists have tended to move from one extreme (i.e. the idea of scala naturae or the existence of a general evolutionary trend in complexity from 'lower' to "higher" taxa, with Homo sapiens as the end stage) to the other, opposite, extreme (i.e. to avoid using terms such as 'phylogenetically basal' and 'anatomically plesiomorphic' taxa, which are seen as the undesired vestige of old teleological theories). The latter view tries to avoid any possible connotations with the original anthropocentric idea of a scala naturae crowned by man and, in that sense, it can be regarded as a more politically correct view. In the past years and months there has been renewed interest in these topics, which have been discussed in various papers and monographs that tend to subscribe, in general, to the points defended in the more politically correct view. Importantly, most evolutionary and phylogenetic studies of tetrapods and other vertebrates, and therefore most discussions on the scala naturae and related issues have been based on hard tissue and, more recently, on molecular data. Here we provide the first discussion of these topics based on a comparative myological study of all the major vertebrate clades and of myological cladistic and Bayesian phylogenetic analyses of bony fish and tetrapods, including Primates. We specifically (i) contradict the notions of a scala naturae or evolutionary progressive trends leading to more complexity in 'higher' animals and culminating in Homo sapiens, and (ii) stress that the refutation of these old notions does not necessarily mean that one should not keep using the terms 'phylogenetically basal' and particularly 'anatomically plesiomorphic' to refer to groups such as the urodeles within the Tetrapoda, or the strepsirrhines and lemurs within the Primates, for instance. This review will contribute to improving our understanding of these broad evolutionary issues and of the evolution of the vertebrate Bauplans, and hopefully will stimulate future phylogenetic, evolutionary and developmental studies of these clades.

Images of cell trees, cell lines, and cell fates: the legacy of Ernst Haeckel and August Weismann in stem cell research

Stem cells did not become a proper research object until the 1960 s. Yet the term and the basic mind-set--namely the conception of single undifferentiated cells, be they embryonic or adult, as the basic units responsible for a directed process of development, differentiation and increasing specialisation--were already in place at the end of the nineteenth century and then transmitted on a non-linear path in the form of tropes and diagrams. Ernst Haeckel and August Weismann played a special role in this story. The first coined the term Stammzelle (stem cell), the second was the author of the first cellular stem-tree diagram. Even today, I shall argue, the understanding of stem cells, especially the popular perception, is to a large extent a Haeckelian-Weismannian one. After having demonstrated this, by analysing the terminology, in this essay I will focus on the use of cytogenetic tree diagrams between 1892 and 1925 and on the tacit understanding of stem cells that they transmit.

Student interpretations of phylogenetic trees in an introductory biology course

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge.

Mathematics and evolutionary biology make bioinformatics education comprehensible

The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

[Tree thinking: the evolution of vertebrate as a case study]

In the last decades, the reconstruction of phylogenetic relationships and their representation in the form of a phylogenetic tree have become a powerful tool for biology. These methods involve the use of sophisticated computer programs that are unfamiliar to most of biologists. However, our experience as teacher and researcher in evolutionary biology prompted us to realize that the main and most common source of confusion in depicting the evolution of various traits comes from the misunderstanding of the basis of tree reading. We have identified, not only in the work of our students, but also in scientific literature, some common mistakes that reveal the persistency of the concept of the scale of beings that unfortunately maintained as frame of reference to analyse phylogenies.

An Update of Wallace’s Zoogeographic Regions of the World

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms

We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.

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.