Research In Evolutionary Biology Research Articles

Speciation Post Synthesis: 1960-2000.

Speciation-the origin of new species-has been one of the most active areas of research in evolutionary biology, both during, and since the Modern Synthesis. While the Modern Synthesis certainly shaped research on speciation in significant ways, providing a core framework, and set of categories and methods to work with, the history of work on speciation since the mid-twentieth century is a history of divergence and diversification. This piece traces this divergence, through both theoretical advances, and empirical insights into how different lineages, with different genetics and ecological conditions, are shaped by very different modes of diversification.

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

For over a decade, DNA barcoding has proven an effective modern tool in taxonomy, evolutionary biology and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. Using DNA barcodes, we uncovered a number of potential species within the Tanytarsus curticornis and Tanytarsus heusdensis species complexes (Diptera: Chironomidae) and detected morphological differences a posteriori that support the description of new species. Unusually large intraspecific divergence in COI p-distance (up to 10%) was observed for two species complexes. In total, eight species new to science are described and figured: T. adustus sp. n., T. heberti sp. n., T. madeiraensis sp. n., T. pseudoheusdensis sp. n., T. songi sp. n., T. thomasi sp. n., T. tongmuensis sp. n. and T. wangi sp. n.. Tanytarsus reei and T. tamaoctavus are redescribed, and T. tusimatneous is listed as a new junior synonym of T. tamaduodecimus. The diagnostic characters of the remaining species of the complexes are discussed. Keys to males and pupae are given.

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome.

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.

Biology Needs Evolutionary Software Tools: Let's Build Them Right.

Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training.

Where is, in 2017, the evo in evo‐devo (evolutionary developmental biology)?

After the inaugural Pan-American-Evo-Devo meeting (2015, Berkeley), I showed how major concerns about evo-devo (Evolutionary Developmental Biology) research were demonstrated by a simple, non-biased quantitative analysis of the titles/abstracts of that meeting's talks. Here, I apply the same methodology to the titles/abstracts of the recent Pan-American-Evo-Devo meeting (2017, Calgary). The aim is to evaluate if the concerns raised by me in that paper and by other authors have been addressed and/or if there are other types of differences between the two meetings that may reflect trends within the field of evo-devo. This analysis shows that the proportion of presentations referring to "morphology", "organism", "selection", "adaptive", "phylogeny", and their derivatives was higher in the 2017 meeting, which therefore had a more "organismal" feel. However, there was a decrease in the use of "evolution"/its derivatives and of macroevolutionary terms related to the tempo and mode of evolution in the 2017 meeting. Moreover, the disproportionately high use of genetic/genomic terms clearly shows that evo-devo continues to be mainly focused on devo, and particularly on "Geno", that is, on molecular/genetic studies. Furthermore, the vast majority of animal evo-devo studies are focused only on hard tissues, which are just a small fraction of the whole organism-for example, only 15% of the tissue mass of the human body. The lack of an integrative approach is also evidenced by the lack of studies addressing conceptual/long-standing broader questions, including the links between ecology and particularly behavior and developmental/evolutionary variability and between evo-devo and evolutionary medicine.

Not Noble Savages After All: Limits to Early Altruism

Many scholars draw on evidence from evolutionary biology, behavioral economics, and infant research to argue that humans are “noble savages,” endowed with indiscriminate kindness. We believe this is mistaken. While there is evidence for an early-emerging moral sense—even infants recognize and favor instances of fairness and kindness among third parties—altruistic behaviors are selective from the start. Babies and young children favor people who have been kind to them in the past and favor familiar individuals over strangers. They hold strong biases for in-group over out-group members and for themselves over others, and indeed are more unequivocally selfish than older children and adults. Much of what is most impressive about adult morality arises not through inborn capacities but through a fraught developmental process that involves exposure to culture and the exercise of rationality.

What have humans done for evolutionary biology? Contributions from genes to populations.

Many fundamental concepts in evolutionary biology were discovered using non-human study systems. Humans are poorly suited to key study designs used to advance this field, and are subject to cultural, technological, and medical influences often considered to restrict the pertinence of human studies to other species and general contexts. Whether studies using current and recent human populations provide insights that have broader biological relevance in evolutionary biology is, therefore, frequently questioned. We first surveyed researchers in evolutionary biology and related fields on their opinions regarding whether studies on contemporary humans can advance evolutionary biology. Almost all 442 participants agreed that humans still evolve, but fewer agreed that this occurs through natural selection. Most agreed that human studies made valuable contributions to evolutionary biology, although those less exposed to human studies expressed more negative views. With a series of examples, we discuss strengths and limitations of evolutionary studies on contemporary humans. These show that human studies provide fundamental insights into evolutionary processes, improve understanding of the biology of many other species, and will make valuable contributions to evolutionary biology in the future.

Perspectives on Integrating Genetic and Physical Explanations of Evolution and Development: An Introduction to the Symposium.

In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium "Physical and Genetic Mechanisms for Evolutionary Novelty" that was dedicated to exploring empirical cases where both biological physics and developmental genetic considerations are crucial. To further contextualize these case studies, we offer two theoretical frameworks for integrating genetic and physical explanations: combining complementary perspectives and comprehensive unification. We conclude by arguing that intentional reflection on conceptual questions about investigation, explanation, and integration is critical to achieving significant empirical and theoretical advances in our understanding of how novel forms originate across the tree of life.

Issue Information

COVER PHOTOGRAPH: Stage 41. Early pre‐hatching. The tip of the tail extends over the head to the posterior of the eye. The iridocytes start to turn a brown‐orange color. A few small round teeth are visible on the jaws. There are 30‐32 cartilaginous vertebrae with neural and hemal arches forming. Ossification of the vertebrae and arches is underway. In the tail, the hypural plate cartilages are forming. From: Embryonic development of the annual killifish Austrofundulus limnaeus: An emerging model for ecological and evolutionary developmental biology research and instruction; Jason E. Podrabsky, Claire L. Riggs, Amie L. Romney, S. Cody Woll, Josiah T. Wagner, Kristin M. Culpepper and Timothy G. Cleaver; Developmental Dynamics 246:779–801.

How apomictic taxa are treated in current taxonomy: A review

AbstractGametophytic apomixis (asexual seed formation without syngamy of female and male gametes) is a highly interesting mechanism for researchers in plant biotechnology, genetics, evolutionary biology, and taxonomy. Apomixis evolved repeatedly and independently in the evolution of multiple genera. It is an effective reproduction barrier and, consequently, conserved apomictic genotypes may become overrepresented in nature. Apomictic plants may easily colonize free niches with only one or a few individuals and outcompete outcrossing plants. In spite of the indisputable pros of asexual reproduction, apomixis also has several cons. One of the most commonly mentioned is the accumulation of deleterious mutations in asexual lineages and decreased genetic variation. However, apomicts in general can be genetically highly diverse. The most common sources of this variation are the accumulation of mutations, hybridization with sexual plants, and facultative apomixis. Facultative apomicts are highly variable in their level of residual sexuality, which increases their genotypic and phenotypic variation. Even in the case of obligate apomicts, gene flow is possible due to functional male meiosis and the production of viable pollen grains by apomicts. Apomixis occurs in plant genera in which hybridization together with polyploidization play an important role in diversification and causes severe problems in taxonomy. How to accommodate apomictic taxa in taxonomic treatments, and understanding what should and what should not be referred to as a species are intriguing questions. This review aims to provide an overview of the main characteristics of “apomictic genera” and the approaches used to treat apomictic taxa within these genera. To achieve this aim, the review was divided into several parts. Firstly, the distinctive features of apomictic reproduction and apomictic taxa are described together with issues related to the taxonomic evaluation of apomictic taxa. The second part discusses approaches in the known apomictic genera, and the final part presents the authors’ view on important points, which need to be taken into account in the classification of apomictic taxa.

Embryonic development of the annual killifish Austrofundulus limnaeus: An emerging model for ecological and evolutionary developmental biology research and instruction.

Austrofundulus limnaeus is an annual killifish from the Maracaibo basin of Venezuela. Annual killifishes are unique among vertebrates in their ability to enter into a state of dormancy at up to three distinct developmental stages termed diapause I, II, and III. These embryos are tolerant of a wide variety of environmental stresses and develop relatively slowly compared with nonannual fishes. These traits make them an excellent model for research on interactions between the genome and the environment during development, and an excellent choice for developmental biology laboratories. Furthermore, A. limnaeus is relatively easy to maintain in a laboratory setting and has a high fecundity, making it an excellent candidate as an emerging model for studies of development, and for defining the limits of developmental buffering in vertebrates. This study reports for the first time on the detailed development of A. limnaeus and provides a photographic and illustrated atlas of embryos on the two developmental trajectories possible in this species. Developmental Dynamics 246:779-801, 2017. © 2017 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.

TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites.

Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique perspective into this task by allowing the detection of associations between sequence evolution rate and whole-organism phenotypes. By analyzing sequences and phenotypes of extant species in the context of their phylogeny, it identifies sequence sites in a gene/protein whose evolutionary rate is associated with shifts in the phenotype. To this end, it considers alternative histories of whole-organism phenotypic changes, which result in the extant phenotypic states. Its joint likelihood framework that combines models of sequence and phenotype evolution allows testing whether an association between these processes exists. In addition to predicting sequence sites most likely to be associated with the phenotypic trait, the server can optionally integrate structural 3D information. This integration allows a visual detection of trait-associated sequence sites that are juxtapose in 3D space, thereby suggesting a common functional role. We used TraitRateProp to study the shifts in sequence evolution rate of the RPS8 protein upon transitions into heterotrophy in Orchidaceae. TraitRateProp is available at http://traitrate.tau.ac.il/prop.

LepNet: The Lepidoptera of North America Network.

The Lepidoptera of North America Network, or LepNet, is a digitization effort recently launched to mobilize biodiversity data from 3 million specimens of butterflies and moths in United States natural history collections (http://www.lep-net.org/). LepNet was initially conceived as a North American effort but the project seeks collaborations with museums and other organizations worldwide. The overall goal is to transform Lepidoptera specimen data into readily available digital formats to foster global research in taxonomy, ecology and evolutionary biology.

Using Xenopus to understand human disease and developmental disorders.

Model animals are crucial to biomedical research. Among the commonly used model animals, the amphibian, Xenopus, has had tremendous impact because of its unique experimental advantages, cost effectiveness, and close evolutionary relationship with mammals as a tetrapod. Over the past 50years, the use of Xenopus has made possible many fundamental contributions to biomedicine, and it is a cornerstone of research in cell biology, developmental biology, evolutionary biology, immunology, molecular biology, neurobiology, and physiology. The prospects for Xenopus as an experimental system are excellent: Xenopus is uniquely well-suited for many contemporary approaches used to study fundamental biological and disease mechanisms. Moreover, recent advances in high throughput DNA sequencing, genome editing, proteomics, and pharmacological screening are easily applicable in Xenopus, enabling rapid functional genomics and human disease modeling at a systems level.

Lifemap: Exploring the Entire Tree of Life.

The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms.

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.

BackgroundTaxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings.ResultsFrom the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix.ConclusionsETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1352-7) contains supplementary material, which is available to authorized users.

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT).

BackgroundDuring recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet.New informationThe Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices.

Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingii

The spectacular threat display of the savannah specialist Australo-Papuan frilled lizards has made them one of the world’s most iconic reptiles. They are increasingly used as a model system for research in evolutionary biology and ecology but little is known of their population structure. Their distribution across northern Australia and southern New Guinea also provides an opportunity to examine biogeographic patterns as they relate to the large-scale movement of savannah habitat during the Plio/Pleistocene and the associated increase in aridity. We generated sequence data for one mitochondrial and four nuclear DNA loci (5052 base pairs) for 83 frilled lizards sampled throughout their range. We also quantified body proportion variation for 279 individuals. Phylogenetic analyses based on maximum likelihood and Bayesian species-tree methods revealed three shallow clades that replace each other across the monsoon tropics. We found the expected pattern of male biased sexual size dimorphism in both maximum body size and head size but there was no sexual dimorphism in overall body shape or in frill size, relative to head size, supporting the hypothesis that the frill is used primarily as a threat display rather than a sexual display. The genetic clades are broadly consistent with known clinal variation in frill color that gradually shifts from west to east (red, orange, yellow/white) but otherwise show little morphological differentiation in body proportion measures. The biogeographic breaks between clades occur at the Carpentaria Gap and the lowlands surrounding the Ord River, and our ecological niche modeling predicts lower habitat suitability for C. kingii in these regions. While this biogeographic pattern is consistent with numerous other taxonomic groups in northern Australia, the overall low genetic diversity in frilled lizards across the entire monsoon tropics and southern New Guinea contrasts starkly to patterns seen in other terrestrial vertebrates. Extremely low intra-clade genetic diversity over vast geographic areas is indicative of recent gene flow that would likely have been facilitated by widespread savannah during interglacials, or alternatively may reflect population bottlenecks induced by extreme aridity during Pleistocene glacials. The shallow divergence between Australian and New Guinean samples is consistent with recent connectivity between Australia and New Guinea that would have been possible via a savannah corridor across the Torres Strait. Based on our molecular and morphological data, we do not support taxonomic recognition of any of the frilled lizard clades and instead consider C. kingii a single species with shallow phylogeographic structure and clinal variation in frill color.

Picking holes in traditional species delimitations: an integrative taxonomic reassessment of theParmotrema perforatumgroup (Parmeliaceae, Ascomycota)

Accurate species delimitation is important as species are a fundamental unit in ecological, evolutionary and conservation biology research. In lichenized fungi, species delimitation has been difficult due to a lack of taxonomically important characteristics and due to the limits of traditional, morphology-based species concepts. In this study we reassess the current taxonomy of the Parmotrema perforatum group, which recognizes six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. It was hypothesized that the three apotheciate species are reproductively isolated sibling species and that each sorediate species evolved once from the chemically identical apotheciate species. In this study, species boundaries were re-examined using an integrative approach incorporating morphological, chemical and molecular sequence data to delimit species boundaries. Phylogenetic trees were inferred from a seven-locus DNA sequence dataset using concatenated gene tree and coalescent-based species-tree inference methods. Furthermore, we employed a multi-species coalescent method to validate candidate species. Micromorphological measurements of conidia were found to be congruent with phylogenetic clusters. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species (P. perforatum, P. hypotropum, P. subrigidum and P. louisianae), whereas P. preperforatum and P. hypoleucinum were consistently combined and are thus interpreted as conspecific.

Revision of the Old World Daphnia (Ctenodaphnia) similis group Cladocera: Daphniidae).

Species of the genus Daphnia O.F. Müller, 1785 (Cladocera: Daphniidae) have become very important models in evolutionary biology research. Previous morphological and genetic evidence suggests that numerous closely related "species groups" exist within the subgenus Daphnia (Ctenodaphnia) Dybowski & Grochowski, 1895, containing both described and undescribed species. The Daphnia similis group is among these species groups. The aim of the present paper is to revise the taxonomy of the Daphnia (Ctenodaphnia) similis group in the Old World with both morphological and genetic evidence (based on mitochondrial COI and 12S rRNA genes). We found that there are at least four species in the Old World D. similis species group: D. similis Claus, 1876; D. sinensis Gu, Xu, Li, Dumont et Han, 2013; D. similoides Hudec, 1991 and D. inopinata sp. nov. These four taxa of the similis-group, confused previously with D. similis, have different distributional ranges in the Old World, from extremely wide, spanning several biogegraphic regions (as D. sinensis), to regional endemics (D. similoides) and even species known so far from a single locality (D. inopinata sp. nov.). The Daphnia similis group provides another example in the cladocerans whereby the study of males yields more valuable characters for taxonomy than the study of parthenogenetic females.