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The laeta species group is the main source of Loxosceles species in Chile, a genus of medical importance due to the cytotoxic properties of its venom and the synanthropic habits of its dominant spe...

During the evening of January 9th, 2020, an adult female of Sicarius thomisoides was found under a rock feeding on a gecko Phyllodactylus gerrhopygus. The observation was made at Mamina, Tamarugal province in northern Chile. This find is the first documented case of a sicariid preying on a vertebrate. Specifically, this event corresponds to a particular case of intraguild predation, since these species are insectivorous and use similar microhabitats in northern Chile

The study of biogeography seeks taxa that share a key set of characteristics, such as timescale of diversification, dispersal ability, and ecological lability. Tarantulas are ideal organisms for studying evolution over continental-scale biogeography given their time period of diversification, their mostly long-lived sedentary lives, low dispersal rate, and their nevertheless wide circumtropical distribution. In tandem with a time-calibrated transcriptome-based phylogeny generated by PhyloBayes, we estimate the ancestral ranges of ancient tarantulas using two methods, DEC+j and BBM, in the context of their evolution. We recover two ecologically distinct tarantula lineages that evolved on the Indian Plate before it collided with Asia, emphasizing the evolutionary significance of the region, and show that both lineages diversified across Asia at different times. The most ancestral tarantulas emerge on the Americas and Africa 120 Ma–105.5 Ma. We provide support for a dual colonization of Asia by two different tarantula lineages that occur at least 20 million years apart, as well as a Gondwanan origin for the group. We determine that their current distributions are attributable to a combination of Gondwanan vicariance, continental rafting, and geographic radiation. We also discuss emergent patterns in tarantula habitat preferences through time.

Tarantulas paradoxically exhibit a diverse palette of vivid colouration despite their crepuscular to nocturnal habits. The evolutionary origin and maintenance of these colours remains a mystery. In this study, we reconstructed the ancestral states of both blue and green colouration in tarantula setae, and tested how these colours correlate with the presence of stridulation, urtication, and arboreality. Green colouration has likely evolved at least eight times, and blue colouration is likely an ancestral condition that appears to be lost more frequently than gained. While our results indicate that neither colour correlates with the presence of stridulation or urtication, the evolution of green colouration appears to depend upon the presence of arboreality, suggesting that it likely originated for, and functions in, crypsis through substrate matching among leaves. We also constructed a network of opsin homologs across tarantula transcriptomes. Despite their crepuscular tendencies, tarantulas express a full suite of opsin genes – a finding that contradicts current consensus that tarantulas have poor colour vision on the basis of low opsin diversity. Overall, our results support the intriguing hypotheses that blue colouration may have ultimately evolved via sexual selection and perhaps proximately be used in mate choice or predation avoidance due to possible sex differences in mate-searching.

Psechrids are an enigmatic family of S.E. Asian spiders. This small family builds sheet webs and even orb webs, yet unlike other orb weavers, its putative relatives are largely cursorial lycosoids - a superfamily of approximately seven spider families related to wolf spiders. The orb web was invented at least twice: first in a very ancient event, and then second, within this clade of wolf-like spiders that reinvented this ability. Exactly how the spiders modified their silks, anatomy, and behaviors to accomplish this transition requires that we identify their precise evolutionary origins - yet, thus far, molecular phylogenies show poor support and considerable disagreement. Using phylogenomic methods based on whole body transcriptomes for psechrids and their putative relatives, we have recovered a well-supported phylogeny that places the Psechridae sister to the Ctenidae - a family of mostly cursorial habits but that, as with all psechrids, retains some cribellate species. Although this position reinforces the prevailing view that orb weaving in psechrids is largely a consequence of convergence, it is still possible that some components of this behavior are retained or resurrected in common with more distant true orb weaving ancestors.

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.

Mygalomorph spiders of the family Theraphosidae, known to the broader public as tarantulas, are among the most recognizable arachnids on earth due to their large size and widespread distribution. Their use of urticating setae is a notable adaptation that has evolved exclusively in certain New World theraphosids. Thus far, the evolutionary history of Theraphosidae remains poorly understood; theraphosid systematics still largely relies on morphological datasets, which suffer from high degrees of homoplasy, and traditional Sanger sequencing of preselected genes failed to provide strong support for supra-generic clades. In this study, we provide the first robust phylogenetic hypothesis of theraphosid evolution inferred from transcriptome data. A core ortholog approach was used to generate a phylogeny from 2460 orthologous genes across 25 theraphosid genera, representing all of the major theraphosid subfamilies, except Selenogyrinae. Our phylogeny recovers an unprecedented monophyletic group that comprises the vast majority of New World theraphosid subfamilies including Aviculariinae, Schismatothelinae and Theraphosinae. Concurrently, we provide additional evidence for the integrity of questionable subfamilies, such as Poecilotheriinae and Psalmopoeinae, and support the non-monophyly of Ischnocolinae. The deeper relationships between almost all subfamilies are confidently inferred. We also used our phylogeny in tandem with published morphological data to perform ancestral state analyses on urticating setae, and contextualize our reconstructions with emphasis on the complex evolutionary history of the trait. © 2019 Elsevier Inc.

Mygalomorph spiders of the family Theraphosidae, known to the broader public as tarantulas, are among the most recognizable arachnids on earth due to their large size and widespread distribution. Their use of urticating setae is a notable adaptation that has evolved exclusively in certain New World theraphosids. Thus far, the evolutionary history of Theraphosidae remains poorly understood; theraphosid systematics still largely relies on morphological datasets, which suffer from high degrees of homoplasy, and traditional targeted sequencing of preselected genes failed to provide strong support for supra-generic clades (i.e. particularly those broader than subfamilies). In this study, we provide the first robust phylogenetic hypothesis of theraphosid evolution inferred from transcriptome data. A core ortholog approach was used to generate a phylogeny from 2460 orthologous genes across 25 theraphosid genera, representing all of the major theraphosid subfamilies, except Selenogyrinae. For the first time our phylogeny recovers a monophyletic group that comprises the vast majority of New World theraphosid subfamilies including Aviculariinae and Theraphosinae. Concurrently, we provide additional evidence for the integrity of questionable subfamilies, such as Poecilotheriinae and Psalmopoeinae, and support the non-monophyly of Ischnocolinae. The deeper relationships between almost all subfamilies are confidently inferred for the first time. We also used our phylogeny in tandem with published morphological data to perform ancestral state analyses on urticating setae. This revealed that the evolution of this important defensive trait might be explained by three equally parsimonious scenarios.

The Distal-less (Dll) genes are homeodomain transcription factors that are present in most Metazoa and in representatives of all investigated arthropod groups. In Drosophila, the best studied insect, Dll plays an essential role in forming the proximodistal axis of the legs, antennae and analia, and in specifying antennal identity. The initiation of Dll expression in clusters of cells in mid-lateral regions of the Drosophila embryo represents the earliest genetic marker of limbs. Dll genes are involved in the development of the peripheral nervous system and sensitive organs, and they also function as master regulators of black pigmentation in some insect lineages. Here we analyze the complete genomes of six insects, the nematode Caenorhabditis elegans and Homo sapiens, as well as multiple Dll sequences available in databases in order to examine the structure and protein features of these genes. We also review the function, expression, regulation and evolution of arthropod Dll genes with emphasis on insects and spiders.

Over the last 20 years, TreeBASE has acquired a substantial body of phylogenetic data, including more than 20,000 published phylogenies. Given latency issues and limited options when it comes to querying the database remotely, a simplified and consolidated version of the database, here called TreeBASEdmp, is made available for download, allowing biologists to design custom analyses of the data on their local computers. The database is indexed to support searching for phylogenetic topologies using nested sets and closure tables. Here we propose a new approach to find broadly-defined phylogenetic patterns, a method we call Generic Topological Querying, which allows the user to find hypotheses of relationship without being constrained to use particular sets of specific taxa. Additionally, we normalize as many leaf nodes as possible to an equivalent species rank identifier to assist in supertree synthesis. Our example script rapidly assembles sets of trees and generates a matrix representation of them for subsequent supertree generation.

Data, whether images, measurements, counts, occurrences, or character codings, are a cornerstone of vertebrate paleontology. Every published paper, master's thesis, and doctoral dissertation relies on these data to document patterns and processes in evolution, ecology, taphonomy, geography, geologic time, and functional morphology, to name just a few. In turn, the vertebrate paleontology community relies on published data in order to reproduce and verify others' work, as well as to expand upon published analyses in new ways without having to reconstitute data sets that have been used by earlier authors and to accurately preserve data for future generations of researchers. Here, we review several databases that are of interest to vertebrate paleontologists and strongly advocate for more deposition of basic research data in publicly accessible databases by vertebrate paleontologists.

The Distal-less (Dll) genes are homeodomain transcription factors that are present in most Metazoa and in representatives of all investigated arthropod groups. In Drosophila, the best studied insect, Dll plays an essential role in forming the proximodistal axis of the legs, antennae and analia, and in specifying antennal identity. The initiation of Dll expression in clusters of cells in mid-lateral regions of the Drosophila embryo represents the earliest genetic marker of limbs. Dll genes are involved in the development of the peripheral nervous system and sensitive organs, and they also function as master regulators of black pigmentation in some insect lineages. Here we analyze the complete genomes of six insects, the nematode Caenorhabditis elegans and Homo sapiens, as well as multiple Dll sequences available in databases in order to examine the structure and protein features of these genes. We also review the function, expression, regulation and evolution of arthropod Dll genes with emphasis on insects and spiders.

Summary Advances in both informatics and mobile technology are providing exciting new opportunities for generating, disseminating, and engaging with information in the biological sciences at unprecedented spatial scales, particularly in disentangling information on the distributions and natural history of hyperdiverse groups of organisms. We describe an application serving as a mobile catalog of all of the plants of the Americas developed using species distribution models estimated from field observations of plant occurrences. The underlying data comprise over 3·5 million standardized observations of over 88 000 plant species. Plant-O-Matic, a free iOS application, combines the species distribution models with the location services built into a mobile device to provide users with a list of all plant species expected to occur in the 100 × 100 km geographic grid cell corresponding to the user's location. The application also provides ancillary information on species’ attributes (when available) including growth form, reproductive mode, flower color, and common name. Results can be searched and conditionally filtered based on these attributes. Links to externally sourced specimen images further aid in identification of species by the user. The application's ability to assemble locally relevant lists of plant species and their attributes on demand for anywhere in the Americas provides a powerful new tool for identifying, exploring, and understanding plant diversity. Mobile applications such as Plant-O-Matic can facilitate dynamic new approaches to science, conservation, and science education.

One of the key hypothesized drivers of gradients in species richness is environmental filtering, where environmental stress limits which species from a larger species pool gain membership in a local community owing to their traits. Whereas most studies focus on small-scale variation in functional traits along environmental gradient, the effect of large-scale environmental filtering is less well understood. Furthermore, it has been rarely tested whether the factors that constrain the niche space limit the total number of coexisting species. We assessed the role of environmental filtering in shaping tree assemblages across North America north of Mexico by testing the hypothesis that colder, drier, or seasonal environments (stressful conditions for most plants) constrain tree trait diversity and thereby limit species richness. We assessed geographic patterns in trait filtering and their relationships to species richness pattern using a comprehensive set of tree range maps. We focused on four key plant functional traits reflecting major life history axes (maximum height, specific leaf area, seed mass, and wood density) and four climatic variables (annual mean and seasonality of temperature and precipitation). We tested for significant spatial shifts in trait means and variances using a null model approach. While we found significant shifts in mean species' trait values at most grid cells, trait variances at most grid cells did not deviate from the null expectation. Measures of environmental harshness (cold, dry, seasonal climates) and lower species richness were weakly associated with a reduction in variance of seed mass and specific leaf area. The pattern in variance of height and wood density was, however, opposite. These findings do not support the hypothesis that more stressful conditions universally limit species and trait diversity in North America. Environmental filtering does, however, structure assemblage composition, by selecting for certain optimum trait values under a given set of conditions.

Knowledge of phylogeny is of fundamental importance for understanding evolution. It has become an indispensable tool in modern genomics as a framework for interpreting genomes and metagenomes, for understanding evolution of genes, proteins, and noncoding RNAs as well as different types of regulations including secondary RNA and protein structures, and for reconstructing ancestral genomes [1]. The era of next-generation sequencing (NGS) brought an influx of data but posed theoretical challenges, for example, in reducing systematic errors and increasing robustness under much less sampling error [2]. An important avenue of modern phylogenetics is the study of coevolution. Here a major focus is the developing of effective algorithms to infer common history of genes, proteins, molecular machines (ribosomes, RNA polymerases, and transporter systems), signal transductions, metabolic pathways, chromosomal structures and gene synteny, and so forth. An important direction is to define and reconstruct the evolutionary scenario on the basis of polytomous trees, also in application to study fast evolving bacteria and viruses with high medical impact, and in shaping the primary genomes. Dating of the phylogeny immediately depends on progress in detecting zones of active horizontal gene transfers or other genomic events, defining time slices to describe tree-like phylogenies, and so forth. Mathematics of phylogenetics will grow to foster alternative ways to describe evolution: generalization of trees into nets and developing models based on stochastic and partial differential equations. An important focus is to develop low polynomial complexity algorithms for exact models that are usually solved heuristically. Contemporary methods of clustering and discrete optimization have already proved very effective. Thus, graphs with 1020 vertices, 109 parts, and the same average vertex degree can be processed on a multiprocessor machine in reasonable time. A high priority for testing modern algorithms is to obtain primary data with known predefined solutions. The call is for realistic computational models that allow simulating large-scale phylogenies and can serve for future studies, as well as real data with known phylogenies or at least few data sets where everybody would agree what the correct phylogeny is. The contents of the special issue of 2015 cover research of various groups that use the toolkit of phylogenetics to tackle a spectrum of evolutionary questions. Apart from classic molecular systematic applications to infer taxon phylogenies, the trend is obvious to approach molecular and biodiversity assessment at different levels in various communities, at intraspecific level and in environmental samples, including systematic studies of bacterial and viral pathogenic agents. Molecular markers such as mobile elements are being developed and exploited in studies of population polymorphisms, and RNA secondary structures are used to detect signatures of selection. A historical profile of molecular phylogenetics with some extrapolations into the future, as well as a brief outline of hot spots in this field, can be found in this special issue [3]. We truly hope that these contributions will be of use to scientists in various areas in possibly helping them to find answers and pose new questions in their own research. Vassily Lyubetsky William H. Piel Peter F. Stadler

HSP90 proteins are important molecular chaperones. Transcriptome and genome analyses revealed that the human HSP90 family includes 17 genes that fall into four classes. A standardized nomenclature for each of these genes is presented here. Classes HSP90AA, HSP90AB, HSP90B, and TRAP contain 7, 6, 3, and 1 genes, respectively. HSP90AA genes mapped onto chromosomes 1, 3, 4, and 11; HSP90AB genes mapped onto 3, 4, 6, 13 and 15; HSP90B genes mapped onto 1, 12, and 15; and the TRAP1 gene mapped onto 16. Six genes, HSP90AA1, HSP90AA2, HSP90N, HSP90AB1, HSP90B1 and TRAP1, were recognized as functional, and the remaining 11 genes were considered putative pseudogenes. Amino acid polymorphic variants were detected for genes HSP90AA1, HSP90AA2, HSP90AB1, HSP90B1, and TRAP1. The structures of these genes and the functional motifs and polymorphic variants of their proteins were documented and the features and functions of their proteins were discussed. Phylogenetic analyses based on both nucleotide and protein data demonstrated that HSP90(AA + AB + B) formed a monophyletic clade, whereas TRAP is a relatively distant paralogue of this clade.

As databases become more pervasive through the biological sciences, various data quality issues regarding data legacy, data uniformity and data duplication arise. Due to the nature of this data, each of these problems is non-trivial. For biological data to be corrected and standardized, new methods and frameworks must be developed. This paper proposes one such framework, called BIO-AJAX, which uses principles from data cleaning to improve data quality in biological information systems, specifically in TreeBASE.

Despite the importance of molecular phylogenetics, few of its assumptions have been tested with real data. It is commonly assumed that nonparametric bootstrap values are an underestimate of the actual support, Bayesian posterior probabilities are an overestimate of the actual support, and among-gene phylogenetic conflict is low. We directly tested these assumptions by using a well-supported yeast reference tree. We found that bootstrap values were not significantly different from accuracy. Bayesian support values were, however, significant overestimates of accuracy but still had low false-positive error rates (0% to 2.8%) at the highest values (>99%). Although we found evidence for a branch-length bias contributing to conflict, there was little evidence for widespread, strongly supported among-gene conflict from bootstraps. The results demonstrate that caution is warranted concerning conclusions of conflict based on the assumption of underestimation for support values in real data.

Molecular systematics is frequently beset with phylogenetic results that are not fully resolved. Researchers either state that the absence of resolution is due to character conflict, explosive speciation, or some combination of the two, but seldom do they carefully examine their data to distinguish between these causes. In this study, we exhaustively analyze a set of nuclear and mitochondrial nucleotide data for the Asian tropical butterfly genus Arhopala so as to highlight the causes of polytomies in the phylogenetic trees, and, as a result, to infer important biological events in the history of this genus. We began by using non-parametric statistical methods to determine whether the ambiguously resolved regions in these trees represent hard or soft polytomies. In addition we determined how this correlated to number of inferred changes on branches, using parametric maximum likelihood estimations. Based on congruent patterns in both mitochondrial and nuclear DNA sequences, we concluded that at two stages in the history of Arhopala there have been accelerated instances of speciation. One event, at the base of the phylogeny, generated many of the groups and subgroups currently recognized in this genus, while a later event generated another major clade consisting of both Oriental and Papuan species groups. Based on comparisons of closely related taxa, the ratio of instantaneous rate of evolution between mitochondrial and nuclear DNA evolution is established at approximately 3:1. The earliest radiation is dated between 7 and 11 Ma by a molecular clock analysis, setting the events generating much of the diversity of Arhopala at well before the Pleistocene. Periodical flooding of the Sunda plateau during interglacial periods was, therefore, not responsible for generating the major divisions in the genus Arhopala. Instead, we hypothesize that large-scale climatic changes taking place in the Miocene have induced the early acceleration in speciation.

The evolutionary history of the snail Arianta arbustorum is controversial. This diverse, polytypic species has two distinct forms: one, with a globular shell and closed umbilicus, is found from lowland to high altitudes; the other, with a depressed shell and open umbilicus, is found at a few scattered, high altitude localities. What is the origin of these two forms? Some believe that the depressed shell is a recent, local, ecotypic adaptation to alpine environments. Others believe that this form is a relic of an ancestral condition that may have survived the Pleistocene glaciations on nunatak-like montane refugia, while the globular shell is a derived condition and its presence at high altitudes follows post-Pleistocene recolonisation. We analysed a portion of the mitochondrial gene cytochrome oxidase I for 100 snails of the species A. arbustorum, three additional Arianta species, and nine outgroup taxa from five genera, in order to understand the phylogeographic history of the species. Despite some confounding artefacts that are likely due to introgression among the morphological forms, the resulting phylogeny shows that the depressed shell is plesiomorphic, while the globular shell is derived. Moreover, their disparate histories suggest that the depressed shell variety survived the glaciations in pockets of alpine refugia, while the globular shell variety recolonised the alpine environment post-glacially.

Butterfly eyespots are known to function in predator deflection and predator intimidation, but it is still unclear what factors cause eyespots to serve one function over the other. Both functions have been demonstrated in different species that varied in eyespot size, eyespot number and wing size, leaving the contribution of each of these factors to butterfly survival unclear. Here, we study how each of these factors contributes to eyespot function by using paper butterfly models, where each factor is varied in turn, and exposing these models to predation in the field. We find that the presence of multiple, small eyespots results in high predation, whereas single large eyespots (larger than 6 mm in diameter) results in low predation. These data indicate that single large eyespots intimidate predators, whereas multiple small eyespots produce a conspicuous, but non-intimidating signal to predators. We propose that eyespots may gain an intimidation function by increasing in size. Our measurements of eyespot size in 255 nymphalid butterfly species show that large eyespots are relatively rare and occur predominantly on ventral wing surfaces. By mapping eyespot size on the phylogeny of the family Nymphalidae, we show that these large eyespots, with a potential intimidation function, are dispersed throughout multiple nymphalid lineages, indicating that phylogeny is not a strong predictor of eyespot size.

Background The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. Results The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. Conclusions We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.

Understanding how novel complex traits originate involves investigating the time of origin of the trait, as well as the origin of its underlying gene regulatory network in a broad comparative phylogenetic framework. The eyespot of nymphalid butterflies has served as an example of a novel complex trait, as multiple genes are expressed during eyespot development. Yet the origins of eyespots remain unknown. Using a dataset of more than 400 images of butterflies with a known phylogeny and gene expression data for five eyespot-associated genes from over twenty species, we tested origin hypotheses for both eyespots and eyespot-associated genes. We show that eyespots evolved once within the family Nymphalidae, approximately 90 million years ago, concurrent with expression of at least three genes associated with early eyespot development. We also show multiple losses of expression of most genes from this early three-gene cluster, without corresponding losses of eyespots. We propose that complex traits, such as eyespots, may have originated via co-option of a large pre-existing complex gene regulatory network that was subsequently streamlined of genes not required to fulfill its novel developmental function., Author Summary Butterfly eyespots play an essential role in natural and sexual selection, yet the evolutionary origins of eyespots and of their underlying gene regulatory network remain unknown. By scoring phenotypes and wing expression of five genes in 399 and 21 nymphalid species, respectively, we tested when eyespots and expression of their associated genes evolved. We found that the origin of eyespots was concurrent with the origin of the gene expression patterns, approximately 90 million years ago. Following this event, many genes expressed in eyespot development were lost in some lineages without a corresponding loss of eyespots, indicating substantial evolution in the cluster of genes associated with eyespots. This finding suggests that complex traits such as butterfly eyespots may initially evolve by re-deploying pre-existing gene regulatory networks, which are subsequently trimmed of genes that are unnecessary in the novel context.

Since its inception some 50 years ago, phylogenetics has permeated nearly every branch of biology. Initially developed to classify objects based on a set of cladistic rules, it has now become the central paradigm of evolutionary biology and a key framework for making sense of a wide range of disciplines [1], such as genomics [2], community ecology [3], epidemiology [4], conservation biology [5], and population dynamics [6], to name just a few. It is a testament to the power of phylogenetic methods that its application has expanded far beyond its original inception, now including the study of human culture, such as language and cultural memes [7]. Phylogenetic principles are used to reconstruct complex ancestral traits of morphological characters, genome structures and their properties, and evolutionary events (like gene duplications, losses, transfers, or chromosomal rearrangements). Phylogeny is also essential to infer gene and protein families, uncover complex population histories in epidemiological and other studies, and understand viral and cell genealogies in medicine and developmental biology. New concepts are developing that tackle various aspects of coevolution, including approaches to defining and algorithmically constructing complex evolutionary scenarios for genetic systems, their regulations, epigenetic and intrinsic factors, noncoding genome elements, sequence primary and secondary structures, the speciation process, and so forth. The growth of phylogenetics is not just in breadth of disciplines, but also in the sheer volume of published phylogenetic results. Some twenty years ago, near-exponential growth in phylogenetic publications had already been noticed [8, 9], a growth that was probably attributable to the advent of powerful computers, PCR, and Sanger sequencing. An update on the assessment of phylogenetic growth (Figure 1) shows that not only is the growth in phylogenetic papers exponential, but more importantly the growth in the percentage of papers that report phylogenetic results is also exponential, indicating its increasing share in scientific research. Journals and databases have worked hard to keep pace with this growth, with the development of data repositories to archive and share data (e.g., TreeBASE, http://treebase.org/ and Dryad, http://datadryad.org/) that would otherwise be inefficient to distribute as supplementary addenda. Figure 1 Growth of phylogenetic publications 1980–2012. Both the number of publications that involve “phylogeny” or “phylogenetic” terms and the proportion of publications appear to grow in a way that approximates exponential ... In the last ten years, the rate of growth of phylogenetic publications has waned somewhat (Figure 1), but with the recent advent of next-generation sequencing (NGS) we anticipate a new flood of phylogenetic results that is commensurate with this explosion of NGS data In addition to the phylogenetic results themselves, we also anticipate the need for new methodological papers to improve efficiencies in sequence assembly, multiple alignment, genome annotation, and pipelining of massive analyses. Computational power is at risk of being outstripped because the volume of NGS data more than doubles each year, outpacing Moore's Law [10]. The limits of computational power portend the need for novel analytical approaches [11], among them “exact models” that avoid heuristics by finding mathematically provable global optima for a function, yet requiring low polynomial complexity, developing effective supertree and divide-and-conquer methods. Other perspective directions include modeling of coevolution as a system of stochastic processes, low-polynomial methods of simultaneous phylogeny and alignment construction, and applying mathematically proved methods to simulate test datasets for benchmarking phylogenetic algorithms. These anticipated advances also need new publishing avenues for dissemination to the scientific community. This special open-access issue, which we hope to be an annual occurrence with Biomed Research International, seeks to meet the anticipated demand for disseminating phylogenetic results and phylogenetic methods. The special issue covers a variety of topics in modern phylogenetics and its applications, from phylogenetic systematics to new methodological developments and reviews. Many authors of the special issue also contributed to the Moscow Conference on Molecular Phylogenetics (http://www.en.molphy.ru/), which is organized biannually by Moscow State University and the Institute for Information Transmission Problems of the Russian Academy of Sciences. The call for papers for the next issue “Molecular Phylogenetics 2014” is now open, and we believe that this series will serve as a platform to exchange ideas and publish research in this actively expanding interdisciplinary field.

TreeBASE is a public repository of peer-reviewed phylogenetic knowledge. Researchers submit their results to TreeBASE when they are writing a manuscript based on them for publication in a suitable journal. The submitted data are assigned permanent, unique identifiers and web addresses that authors can refer to in their article. Anyone can locate and access the data once the study has been published by TreeBASE and by the targeted journal. A prototype of this system has served the phylogenetics community well for a number of years, accumulating the results of thousands of studies. The usage model was that of a silo where data could only be accessed through a web browser, and only be downloaded in representations that omitted important associated metadata. A human with considerable expertise needed to read and interpret the web pages through which everything was served up to make sense out of what was available. This model is not always practical. For example, phyloinformatic research often uses so much data that automation is becoming necessary. Where human intervention is no longer feasible, machines – which are stupid – must be able to do the job instead; and they need to be told what is what. This has spurred more explicit standardization of the syntax and semantics of phylogenetic knowledge. The latest version of TreeBASE facilitates this by adopting a collection of community standards: * PhyloWS for automated searching using a contextual query language and retrieval using a clearly defined URL API. * NeXML for robust data syntax and flexible metadata annotation. * CDAO (and other ontologies) for defining the semantics of the metadata. We will present an overview of how these components work together to make phylogenetic knowledge accessible to machines on the semantic web. Using this new architecture, client side software (including off-the-shelve tools such as RSS readers) can query, transform and download TreeBASE data autonomously.

As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P. The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising.

Currently, phylogenetic tree techniques are being used in multiple areas, from tree of life problems to pathogen recognition to drug discovery. With all of these applications for phylogenetic tree techniques, methods are needed to exploit the knowledge modeled in phylogenetic trees more thoroughly. One such information point of interest is the behavior of frequent patterns in phylogenetic trees. While there are many techniques that look at maximal, consensus and super tree patterns, there are few techniques that look at frequent, but not maximal pattern. This demonstration paper presents PhyloMiner, a tool that automatically discovers frequent agreement subtrees from multiple phytogenies. It introduces this topic of frequent agreement subtrees and then concludes with describing the PhyloMiner tool that implements these concepts and is available freely on the World Wide Web

Phylogenetic trees are unordered labeled trees in which each leaf node has a label and the order among siblings is unimportant. In this paper we propose a new similarity measure, called TreeRank, for phylogenetic trees and present an algorithm for computing TreeRank scores. Given a query or pattern tree P and a data tree D, the TreeRank score from P to D is a measure of the topological relationships in P that are found to be the same or similar in D. The proposed algorithm calculates the TreeRank score in O(M/sup 2/ + N) time where M is the number of nodes appearing in both P and D, and N is the number of nodes in D. We then develop a search engine that, given a query or pattern tree P and a database of trees D, finds and ranks the nearest neighbors of P in D where the "nearness" is measured by the proposed similarity function. This structure-based search engine is fully operational and is available on the World Wide Web.

Phylogenetic trees are essential for understanding the relationships among organisms or taxa. Many of the current techniques for searching phylogenetic repositories allow the user to perform a keyword-type search or an aligned sequence data search, or to browse a hierarchical list of taxa. Here we describe a new search engine that allows the user to present an example phylogeny, or a query tree, and then searches a phylogenetic database for trees that contain the query structure. The presented search engine is fully operational and is available on the World Wide Web.

Motivation: A noble and ultimate objective of phyloinformatic research is to assemble, synthesize, and explore the evolutionary history of life on earth. Data mining methods for performing these tasks are not yet well developed, but one avenue of research suggests that network connectivity dynamics will play an important role in future methods. Analysis of disordered networks, such as small-world networks, has applications as diverse as disease propagation, collaborative networks, and power grids. Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies Results: Analyses of tree network connectivity in TreeBASE show that a collection of phylogenetic trees behaves as a small-world network—while on the one hand the trees are clustered, like a non-random lattice, on the other hand they have short characteristic path lengths, like a random graph. Tree connectivities follow a dual-scale power-law distribution (first power-law exponent ≈1.87; second ≈4.82). This unusual pattern is due, in part, to the presence of alternative tree topologies that enter the database with each published study. As expected, small collections of trees decrease connectivity as new trees are added, while large collections of trees increase connectivity. However, the inflection point is surprisingly low: after about 600 trees the network suddenly jumps to a higher level of coherence. More stringent definitions of ‘neighbour’ greatly delay the threshold whence a database achieves sufficient maturity for a coherent network to emerge. However, more stringent definitions of ‘neighbour’ would also likely show improved focus in data mining Availability: http://treebase.org Contact: wpiel@buffalo.edu * To whom correspondence should be addressed. † Current address: Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA

Serial homologues are repeated traits that share similar development but occur in different parts of the body. Variation in number of repeats accounts for substantial diversity in animal form and considerable work has focused on identifying the factors accounting for this variation. Little is known, however, about how serial homologues originally become repeated, or about the relative timing of repeat individuation relative to repeat origin. Here, we show that the serially repeated eyespots on nymphalid butterfly wings most likely arose as a small cluster of units on the ventral hindwing that were later co-opted to the dorsal and anterior wing surfaces. Based on comparative analyses of over 400 species, we found support for a model of eyespot origin followed by redeployment, rather than by the conventional model, where eyespots arose as a complete row of undifferentiated units that later gained individuation. In addition, eyespots most likely evolved from simpler pattern elements, single-coloured spots, which were already individuated among different wing sectors. Finally, the late appearance of eyespots on the dorsal, hidden wing surface further suggests that these novel complex traits originally evolved for one function (thwarting predator attacks) and acquired a second function (sexual signalling) when moved to a different body location. This broad comparative analysis illustrates how serial homologues may initially evolve as a few units serving a particular function and subsequently become repeated in novel body locations with new functions.

Paradoxically, an allozyme study of Metepeira “spinipes” (sensu lato) demonstrated extensive gene flow among four populations whose members are nevertheless morphologically and behaviorally distinct. Initially, the authors tentatively concluded that the populations exhibited panmixis and suggested that local environmental effects accounted for the apparent morphological and behavioral differences. However, they later concluded that such differences were too great to be accounted for by the environment alone and that the four populations actually represented three different species. To confirm that the allozyme results were, in fact, artifactual, we reexamined the relationships among these populations by sequencing a portion of the 12S mtDNA ribosomal subunit. In contrast to the allozyme result, our results demonstrate good agreement between patterns of genetic and morphological/behavioral variation. We suggest (1) that the allozyme allele frequencies are homogenized by balancing selection, not gene flow as was previously concluded, and therefore (2) that this study provides another instance in which inferences about population structures from allozyme data are misleading.

Summary: PhyloWidget is a web-based tool for the visualization and manipulation of phylogenetic tree data. It can be accessed online or downloaded as a standalone application. A simple URL-based API allows databases to easily link to and customize PhyloWidget for interactively viewing medium- to large-sized trees. Availability: PhyloWidget is available for online use or download at http://www.phylowidget.org/. Its source code is released under the GNU General Public License. Contact: phylowidget@treebase.org

This report summarizes the proceedings of the second workshop of the ‘Minimum Information for Biological and Biomedical Investigations’ (MIBBI) consortium held on Dec 1–2, 2010 in Rudesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/ .