Botanical Gardens Are Local Hotspots for Urban Butterflies in Arid Environments.

Urban areas are proliferating quickly around the globe often with detrimental impacts on biodiversity. Insects, especially pollinators, have also seen record declines in recent decades, sometimes associated with land use change such as urbanization, but also associated with climate changes such as increased aridity. How these various factors play out in attracting and sustaining species richness in a complex urban matrix is poorly understood. Urban botanical gardens may serve as important refugia for insect pollinators in arid regions due to reliable water availability for both plants and insects. Here, we use community science data on butterfly observations to evaluate if botanical gardens can be hotspots of biodiversity in the arid urban landscapes of the southwest US. We found butterfly richness and diversity were proportionally overrepresented in botanical gardens compared with the urban landscape they were embedded in. We conclude that biodiversity-friendly botanical gardens in urban arid regions can make a valuable contribution to pollinator conservation, in particular, in face of the continued aridification due to climate change.

Undergraduate data science degrees emphasize computer science and statistics but fall short in ethics training and domain-specific context.

The interdisciplinary field of data science, which applies techniques from computer science and statistics to address questions across domains, has enjoyed recent considerable growth and interest. This emergence also extends to undergraduate education, whereby a growing number of institutions now offer degree programs in data science. However, there is considerable variation in what the field actually entails and, by extension, differences in how undergraduate programs prepare students for data-intensive careers. We used two seminal frameworks for data science education to evaluate undergraduate data science programs at a subset of 4-year institutions in the United States; developing and applying a rubric, we assessed how well each program met the guidelines of each of the frameworks. Most programs scored high in statistics and computer science and low in domain-specific education, ethics, and areas of communication. Moreover, the academic unit administering the degree program significantly influenced the course-load distribution of computer science and statistics/mathematics courses. We conclude that current data science undergraduate programs provide solid grounding in computational and statistical approaches, yet may not deliver sufficient context in terms of domain knowledge and ethical considerations necessary for appropriate data science applications. Additional refinement of the expectations for undergraduate data science education is warranted.

Origin of the mechanism of phenotypic plasticity in satyrid butterfly eyespots.

Plasticity is often regarded as a derived adaptation to help organisms survive in variable but predictable environments, however, we currently lack a rigorous, mechanistic examination of how plasticity evolves in a large comparative framework. Here, we show that phenotypic plasticity in eyespot size in response to environmental temperature observed in Bicyclus anynana satyrid butterflies is a complex derived adaptation of this lineage. By reconstructing the evolution of known physiological and molecular components of eyespot size plasticity in a comparative framework, we showed that 20E titer plasticity in response to temperature is a pre-adaptation shared by all butterfly species examined, whereas expression of EcR in eyespot centers, and eyespot sensitivity to 20E, are both derived traits found only in a subset of species with eyespots.

A well-known family of butterflies have circular patterns on their wings that look like eyes. These eye-like markings help deflect predators away from the butterfly's body so they attack the outer edges of their wings. However, in certain seasons, such as the dry season in Africa, the best way for this family to survive is by not drawing any attention to their bodies. Thus, butterflies born during this season shrink the size of their eyespots so they can hide among the dry leaves. How this family of butterflies are able to change the size of these eye-like spots has only been studied in the species Bicyclus anynana. During development low temperatures, which signify the beginning of the dry season, reduce the amount of a hormone called 20E circulating in the blood of this species. This changes the behavior of hormone-sensitive cells in the eyespots making them smaller in size. But it remains unclear how B. anynana evolved this remarkable tactic and whether its relatives have similar abilities. Now, Bhardwaj et al. show that B. anynana is the only one of its relatives that can amend the size of its eyespots in response to temperature changes. In the experiments, 13 different species of butterflies, mostly from the family that has eyespots, were developed under two different temperatures. Low temperatures caused 20E hormone levels to decrease in all 13 species. However, most of these species did not develop smaller eyespots in response to this temperature change. This includes species that are known to have larger and smaller eyespots depending on the season. Like B. anynana, four of the species studied have receptors for the 20E hormone at the center of their eyespots. However, changing 20E hormone levels in these species did not reduce eyespot size. These results show that although temperature changes alter hormone levels in a number of species, only B. anynana have taken advantage of this mechanism to regulate eyespot size. In addition, Bhardwaj et al. found that this unique mechanism evolved from several genetic changes over millions of years. Other species likely use other environmental cues to trigger seasonal changes in the size of their eyespots.

Creating the Urban Farmer's Almanac with Citizen Science Data.

Agriculture has long been a part of the urban landscape, from gardens to small scale farms. In recent decades, interest in producing food in cities has grown dramatically, with an estimated 30% of the global urban population engaged in some form of food production. Identifying and managing the insect biodiversity found on city farms is a complex task often requiring years of study and specialization, especially in urban landscapes which have a complicated tapestry of fragmentation, diversity, pollution, and introduced species. Supporting urban growers with relevant data informs insect management decision-making for both growers and their neighbors, yet this information can be difficult to come by. In this study, we introduced several web-based citizen science programs that can connect growers with useful data products and people to help with the who, what, where, and when of urban insects. Combining the power of citizen science volunteers with the efforts of urban farmers can result in a clearer picture of the diversity and ecosystem services in play, limited insecticide use, and enhanced non-chemical alternatives. Connecting urban farming practices with citizen science programs also demonstrates the ecosystem value of urban agriculture and engages more citizens with the topics of food production, security, and justice in their communities.

Mimicry in viceroy butterflies is dependent on abundance of the model queen butterfly.

Mimics should not exist without their models, yet often they do. In the system involving queen and viceroy butterflies, the viceroy is both mimic and co-model depending on the local abundance of the model, the queen. Here, we integrate population surveys, chemical analyses, and predator behavior assays to demonstrate how mimics may persist in locations with low-model abundance. As the queen becomes less locally abundant, the viceroy becomes more chemically defended and unpalatable to predators. However, the observed changes in viceroy chemical defense and palatability are not attributable to differing host plant chemical defense profiles. Our results suggest that mimetic viceroy populations are maintained at localities of low-model abundance through an increase in their toxicity. Sharing the burden of predator education in some places but not others may also lower the fitness cost of warning signals thereby supporting the origin and maintenance of aposematism.

Comparisons of Citizen Science Data-Gathering Approaches to Evaluate Urban Butterfly Diversity.

By 2030, ten percent of earth's landmass will be occupied by cities. Urban environments can be home to many plants and animals, but surveying and estimating biodiversity in these spaces is complicated by a heterogeneous built environment where access and landscaping are highly variable due to human activity. Citizen science approaches may be the best way to assess urban biodiversity, but little is known about their relative effectiveness and efficiency. Here, we compare three techniques for acquiring data on butterfly (Lepidoptera: Rhopalocera) species richness: trained volunteer Pollard walks, Malaise trapping with expert identification, and crowd-sourced iNaturalist observations. A total of 30 butterfly species were observed; 27 (90%) were recorded by Pollard walk observers, 18 (60%) were found in Malaise traps, and 22 (73%) were reported by iNaturalist observers. Pollard walks reported the highest butterfly species richness, followed by iNaturalist and then Malaise traps during the four-month time period. Pollard walks also had significantly higher species diversity than Malaise traps.

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies.

Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis of structurally variable and hyperpolymorphic regions of the genome. In most existing approaches, graphs are constructed from variant call sets derived from short-read sequencing. As long-read sequencing becomes more cost-effective and enables de novo assembly for increasing numbers of whole genomes, a method for the direct construction of a genome graph from sets of assembled human genomes would be desirable. Such assembly-based genome graphs would encompass the wide spectrum of genetic variation accessible to long-read-based de novo assembly, including large structural variants and divergent haplotypes. Here we present NovoGraph, a method for the construction of a human genome graph directly from a set of de novo assemblies. NovoGraph constructs a genome-wide multiple sequence alignment of all input contigs and creates a graph by merging the input sequences at positions that are both homologous and sequence-identical. NovoGraph outputs resulting graphs in VCF format that can be loaded into third-party genome graph toolkits. To demonstrate NovoGraph, we construct a genome graph with 23,478,835 variant sites and 30,582,795 variant alleles from de novo assemblies of seven ethnically diverse human genomes (AK1, CHM1, CHM13, HG003, HG004, HX1, NA19240). Initial evaluations show that mapping against the constructed graph reduces the average mismatch rate of reads from sample NA12878 by approximately 0.2%, albeit at a slightly increased rate of reads that remain unmapped.

Corrigendum to "A Survey of Eyespot Sexual Dimorphism across Nymphalid Butterflies".

[This corrects the article DOI: 10.1155/2013/926702.].

Bioinformatic training needs at a health sciences campus.

BACKGROUND: Health sciences research is increasingly focusing on big data applications, such as genomic technologies and precision medicine, to address key issues in human health. These approaches rely on biological data repositories and bioinformatic analyses, both of which are growing rapidly in size and scope. Libraries play a key role in supporting researchers in navigating these and other information resources. METHODS: With the goal of supporting bioinformatics research in the health sciences, the University of Arizona Health Sciences Library established a Bioinformation program. To shape the support provided by the library, I developed and administered a needs assessment survey to the University of Arizona Health Sciences campus in Tucson, Arizona. The survey was designed to identify the training topics of interest to health sciences researchers and the preferred modes of training. RESULTS: Survey respondents expressed an interest in a broad array of potential training topics, including "traditional" information seeking as well as interest in analytical training. Of particular interest were training in transcriptomic tools and the use of databases linking genotypes and phenotypes. Staff were most interested in bioinformatics training topics, while faculty were the least interested. Hands-on workshops were significantly preferred over any other mode of training. The University of Arizona Health Sciences Library is meeting those needs through internal programming and external partnerships. CONCLUSION: The results of the survey demonstrate a keen interest in a variety of bioinformatic resources; the challenge to the library is how to address those training needs. The mode of support depends largely on library staff expertise in the numerous subject-specific databases and tools. Librarian-led bioinformatic training sessions provide opportunities for engagement with researchers at multiple points of the research life cycle. When training needs exceed library capacity, partnering with intramural and extramural units will be crucial in library support of health sciences bioinformatic research.

eButterfly: Leveraging Massive Online Citizen Science for Butterfly Consevation.

Data collection, storage, analysis, visualization, and dissemination are changing rapidly due to advances in new technologies driven by computer science and universal access to the internet. These technologies and web connections place human observers front and center in citizen science-driven research and are critical in generating new discoveries and innovation in such fields as astronomy, biodiversity, and meteorology. Research projects utilizing a citizen science approach address scientific problems at regional, continental, and even global scales otherwise impossible for a single lab or even a small collection of academic researchers. Here we describe eButterfly an integrative checklist-based butterfly monitoring and database web-platform that leverages the skills and knowledge of recreational butterfly enthusiasts to create a globally accessible unified database of butterfly observations across North America. Citizen scientists, conservationists, policy makers, and scientists are using eButterfly data to better understand the biological patterns of butterfly species diversity and how environmental conditions shape these patterns in space and time. eButterfly in collaboration with thousands of butterfly enthusiasts has created a near real-time butterfly data resource producing tens of thousands of observations per year open to all to share and explore.

Nymphalid eyespots are co-opted to novel wing locations following a similar pattern in independent lineages.

BACKGROUND: Variation in the number of repeated traits, or serial homologs, has contributed greatly to animal body plan diversity. Eyespot color patterns of nymphalid butterflies, like arthropod and vertebrate limbs, are an example of serial homologs. These eyespot color patterns originated in a small number of wing sectors on the ventral hindwing surface and later appeared in novel wing sectors, novel wings, and novel wing surfaces. However, the details of how eyespots were co-opted to these novel wing locations are currently unknown. RESULTS: We used a large data matrix of eyespot/presence absence data, previously assembled from photographs of contemporary species, to perform a phylogenetic investigation of eyespot origins in nine independent nymphalid lineages. To determine how the eyespot gene regulatory network acquired novel positional information, we used phylogenetic correlation analyses to test for non-independence in the origination of eyespots. We found consistent patterns of eyespot gene network redeployment in the nine lineages, where eyespots first redeployed from the ventral hindwing to the ventral forewing, then to new sectors within the ventral wing surface, and finally to the dorsal wing surface. Eyespots that appeared in novel wing sectors modified the positional information of their serial homolog ancestors in one of two ways: by changing the wing or surface identity while retaining sector identity, or by changing the sector identity while retaining wing and surface identity. CONCLUSIONS: Eyespot redeployment to novel sectors, wings, and surfaces happened multiple times in different nymphalid subfamilies following a similar pattern. This indicates that parallel mutations altering expression of the eyespot gene regulatory network led to its co-option to novel wing locations over time.

Nymphalid eyespot serial homologues originate as a few individualized modules.

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.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

Temporal gene expression variation associated with eyespot size plasticity in Bicyclus anynana.

Seasonal polyphenism demonstrates an organism's ability to respond to predictable environmental variation with alternative phenotypes, each presumably better suited to its respective environment. However, the molecular mechanisms linking environmental variation to alternative phenotypes via shifts in development remain relatively unknown. Here we investigate temporal gene expression variation in the seasonally polyphenic butterfly Bicyclus anynana. This species shows drastic changes in eyespot size depending on the temperature experienced during larval development. The wet season form (larvae reared over 24°C) has large ventral wing eyespots while the dry season form (larvae reared under 19°C) has much smaller eyespots. We compared the expression of three proteins, Notch, Engrailed, and Distal-less, in the future eyespot centers of the two forms to determine if eyespot size variation is associated with heterochronic shifts in the onset of their expression. For two of these proteins, Notch and Engrailed, expression in eyespot centers occurred earlier in dry season than in wet season larvae, while Distal-less showed no temporal difference between the two forms. These results suggest that differences between dry and wet season adult wings could be due to a delay in the onset of expression of these eyespot-associated genes. Early in eyespot development, Notch and Engrailed may be functioning as repressors rather than activators of the eyespot gene network. Alternatively, temporal variation in the onset of early expressed genes between forms may have no functional consequences to eyespot size regulation and may indicate the presence of an 'hourglass' model of development in butterfly eyespots.

Microevolutionary processes generate phylogenomic discordance at ancient divergences.

Stochastic population processes may cause differences between species histories and gene histories. These processes are assumed to only influence the most recent divergences in the tree of life; however, there may be underappreciated potential for microevolutionary processes to impact deep divergences. I used multispecies coalescent models to determine the impact of stochastic processes on deep phylogenomic histories. Here I show phylogenomic discordance between gene histories and species histories is expected at deep divergences for many eukaryotic taxa, and the probability of discordance increases with population size, generation time, and the number of species in the tree. Five eukaryotic clades (angiosperms, birds, harpaline beetles, mammals, and nymphalid butterflies) demonstrate significant discordance potential at divergences over 50 million years old, and this discordance potential is independent of the age of divergence. These findings demonstrate population processes acting over very short timescales will leave a lasting impact on genomic histories, even for divergence events occurring tens to hundreds of millions of years ago.

Distal-less regulates eyespot patterns and melanization in Bicyclus butterflies.

Butterfly eyespots represent novel complex traits that display substantial diversity in number and size within and across species. Correlative gene expression studies have implicated a large suite of transcription factors, including Distal-less (Dll), Engrailed (En), and Spalt (Sal), in eyespot development in butterflies, but direct evidence testing the function of any of these proteins is still missing. Here we show that the characteristic two-eyespot pattern of wildtype Bicyclus anynana forewings is correlated with dynamic progression of Dll, En, and Sal expression in larval wings from four spots to two spots, whereas no such decline in gene expression ensues in a four-eyespot mutant. We then conduct transgenic experiments testing whether over-expression of any of these genes in a wild-type genetic background is sufficient to induce eyespot differentiation in these pre-patterned wing compartments. We also produce a Dll-RNAi transgenic line to test how Dll down-regulation affects eyespot development. Finally we test how ectopic expression of these genes during the pupal stages of development alters adults color patters. We show that over-expressing Dll in larvae is sufficient to induce the differentiation of additional eyespots and increase the size of eyespots, whereas down-regulating Dll leads to a decrease in eyespot size. Furthermore, ectopic expression of Dll in the early pupal wing led to the appearance of ectopic patches of black scales. We conclude that Dll is a positive regulator of focal differentiation and eyespot signaling and that this gene is also a possible selector gene for scale melanization in butterflies.

A Survey of Eyespot Sexual Dimorphism across Nymphalid Butterflies.

Differences between sexes of the same species are widespread and are variable in nature. While it is often assumed that males are more ornamented than females, in the nymphalid butterfly genus Bicyclus, females have, on average, more eyespot wing color patterns than males. Here we extend these studies by surveying eyespot pattern sexual dimorphism across the Nymphalidae family of butterflies. Eyespot presence or absence was scored from a total of 38 wing compartments for two males and two females of each of 450 nymphalid species belonging to 399 different genera. Differences in eyespot number between sexes of each species were tallied for each wing surface (e.g., dorsal and ventral) of forewings and hindwings. In roughly 44% of the species with eyespots, females had more eyespots than males, in 34%, males had more eyespots than females, and, in the remaining 22% of the species, there was monomorphism in eyespot number. Dorsal and forewing surfaces were less patterned, but proportionally more dimorphic, than ventral and hindwing surfaces, respectively. In addition, wing compartments that frequently displayed eyespots were among the least sexually dimorphic. This survey suggests that dimorphism arises predominantly in "hidden" or "private" surfaces of a butterfly's wing, as previously demonstrated for the genus Bicyclus.

A single origin for nymphalid butterfly eyespots followed by widespread loss of associated gene expression.

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.

Evolutionary reduction of the first thoracic limb in butterflies.

Members of the diverse butterfly families Nymphalidae (brush-footed butterflies) and Riodinidae (metalmarks) have reduced first thoracic limbs and only use two pairs of legs for walking. In order to address questions about the detailed morphology and evolutionary origins of these reduced limbs, the three thoracic limbs of 13 species of butterflies representing all six butterfly families were examined and measured, and ancestral limb sizes were reconstructed for males and females separately. Differences in limb size across butterflies involve changes in limb segment size rather than number of limb segments. Reduction of the first limb in both nymphalids and riodinids appears particularly extensive in the femur, but the evolution of these reduced limbs is suggested to be a convergent evolutionary event. Possible developmental differences as well as ecological factors driving the evolution of reduced limbs are discussed.

Integrating fossil preservation biases in the selection of calibrations for molecular divergence time estimation.

The selection of fossil data to use as calibration age priors in molecular divergence time estimates inherently links neontological methods with paleontological theory. However, few neontological studies have taken into account the possibility of a taphonomic bias in the fossil record when developing approaches to fossil calibration selection. The Sppil-Rongis effect may bias the first appearance of a lineage toward the recent causing most objective calibration selection approaches to erroneously exclude appropriate calibrations or to incorporate multiple calibrations that are too young to accurately represent the divergence times of target lineages. Using turtles as a case study, we develop a Bayesian extension to the fossil selection approach developed by Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibrations points. Am. Nat. 171:726-742) that takes into account this taphonomic bias. Our method has the advantage of identifying calibrations that may bias age estimates to be too recent while incorporating uncertainty in phylogenetic parameter estimates such as tree topology and branch lengths. Additionally, this method is easily adapted to assess the consistency of potential calibrations to any one calibration in the candidate pool.