recolorize: An R package for flexible colour segmentation of biological images.

Colour pattern variation provides biological information in fields ranging from disease ecology to speciation dynamics. Comparing colour pattern geometries across images requires colour segmentation, where pixels in an image are assigned to one of a set of colour classes shared by all images. Manual methods for colour segmentation are slow and subjective, while automated methods can struggle with high technical variation in aggregate image sets. We present recolorize, an R package toolbox for human-subjective colour segmentation with functions for batch-processing low-variation image sets and additional tools for handling images from diverse (high-variation) sources. The package also includes export options for a variety of formats and colour analysis packages. This paper illustrates recolorize for three example datasets, including high variation, batch processing and combining with reflectance spectra, and demonstrates the downstream use of methods that rely on this output.

Jewel Beetle Opsin Duplication and Divergence Is the Mechanism for Diverse Spectral Sensitivities.

The evolutionary history of visual genes in Coleoptera differs from other well-studied insect orders, such as Lepidoptera and Diptera, as beetles have lost the widely conserved short-wavelength (SW) insect opsin gene that typically underpins sensitivity to blue light (∼440 nm). Duplications of the ancestral ultraviolet (UV) and long-wavelength (LW) opsins have occurred in many beetle lineages and have been proposed as an evolutionary route for expanded spectral sensitivity. The jewel beetles (Buprestidae) are a highly ecologically diverse and colorful family of beetles that use color cues for mate and host detection. In addition, there is evidence that buprestids have complex spectral sensitivity with up to five photoreceptor classes. Previous work suggested that opsin duplication and subfunctionalization of the two ancestral buprestid opsins, UV and LW, has expanded sensitivity to different regions of the light spectrum, but this has not yet been tested. We show that both duplications are likely unique to Buprestidae or the wider superfamily of Buprestoidea. To directly test photopigment sensitivity, we expressed buprestid opsins from two Chrysochroa species in Drosophila melanogaster and functionally characterized each photopigment type as UV- (356-357 nm), blue- (431-442 nm), green- (507-509 nm), and orange-sensitive (572-584 nm). As these novel opsin duplicates result in significantly shifted spectral sensitivities from the ancestral copies, we explored spectral tuning at four candidate sites using site-directed mutagenesis. This is the first study to directly test opsin spectral tuning mechanisms in the diverse and specious beetles.

A cure for the blues: opsin duplication and subfunctionalization for short-wavelength sensitivity in jewel beetles (Coleoptera: Buprestidae).

BACKGROUND: Arthropods have received much attention as a model for studying opsin evolution in invertebrates. Yet, relatively few studies have investigated the diversity of opsin proteins that underlie spectral sensitivity of the visual pigments within the diverse beetles (Insecta: Coleoptera). Previous work has demonstrated that beetles appear to lack the short-wavelength-sensitive (SWS) opsin class that typically confers sensitivity to the "blue" region of the light spectrum. However, this is contrary to established physiological data in a number of Coleoptera. To explore potential adaptations at the molecular level that may compensate for the loss of the SWS opsin, we carried out an exploration of the opsin proteins within a group of beetles (Buprestidae) where short-wave sensitivity has been demonstrated. RNA-seq data were generated to identify opsin proteins from nine taxa comprising six buprestid species (including three male/female pairs) across four subfamilies. Structural analyses of recovered opsins were conducted and compared to opsin sequences in other insects across the main opsin classes-ultraviolet, short-wavelength, and long-wavelength. RESULTS: All nine buprestids were found to express two opsin copies in each of the ultraviolet and long-wavelength classes, contrary to the single copies recovered in all other molecular studies of adult beetle opsin expression. No SWS opsin class was recovered. Furthermore, the male Agrilus planipennis (emerald ash borer-EAB) expressed a third LWS opsin at low levels that is presumed to be a larval copy. Subsequent homology and structural analyses identified multiple amino acid substitutions in the UVS and LWS copies that could confer short-wavelength sensitivity. CONCLUSIONS: This work is the first to compare expressed opsin genes against known electrophysiological data that demonstrate multiple peak sensitivities in Coleoptera. We report the first instance of opsin duplication in adult beetles, which occurs in both the UVS and LWS opsin classes. Through structural comparisons of known insect opsins, we suggest that opsin duplication and amino acid variation within the chromophore binding pocket explains sensitivity in the short-wavelength portion of the visible light spectrum in these species. These findings are the first to reveal molecular complexity of the color vision system within beetles.

Illustrated catalogue and type designations of the New Zealand Zopheridae (Coleoptera: Tenebrionoidea).

This paper provides a comprehensive catalogue of the New Zealand members of the family Zopheridae Solier (Coleoptera: Tenebrionoidea) in an effort to stabilize the nomenclature preceding extensive revisionary taxonomy within the group. A checklist of the 17 New Zealand zopherid genera and an account for each of the 189 species (by current combination) is provided. Type material for nearly all species was examined, and type specimens are designated herein (90 confirmed holotypes, 3 confirmed paratypes, 102 lectotypes, 280 paralectotypes). Images of all primary type specimens and labels examined are provided. Pycnomerus sulcatissimus Sharp, 1886 is a junior synonym and secondary homonym of Pycnomerus sulcatissimus (Reitter, 1880). One replacement name is proposed, Chorasus buckleyi new name, for Chorasus subcaecus (Broun), and 23 new combinations are given.

Evaluation of Hemp (Cannabis sativa) (Rosales: Cannabaceae) as an Alternative Host Plant for Polyphagous Noctuid Pests.

Hemp (Cannabis sativa L.) is a reemerging crop in the United States with increasing outdoor acreage in many states. This crop offers a potential host for polyphagous, defoliating lepidopteran pests currently present in Louisiana. The ability of soybean looper [Chrysodeixis includens (Walker)] (Lepidoptera: Noctuidae), fall armyworm [Spodoptera frugiperda (J.E. Smith)] (Lepidoptera: Noctuidae), and beet armyworm [Spodoptera exigua (Hübner)] to develop and reproduce on hemp was investigated in this study. Insects were reared on two hemp varieties, Maverick and Pipeline, as well as documented host plants soybean [Glycine max (L.) Merr.] (Fabales: Fabaceae) variety UA5414RR and cowpea [Vigna unguiculata (L.)] (Fabales: Fabaceae) variety Quickpick Pinkeye. Larvae of all three species reared on 'Maverick' had significantly faster preadult developmental times compared to the other hosts. Chrysodeixis includens larvae fed excised leaves of 'Maverick' and 'Pipeline' experienced higher intrinsic and finite rates of increase, higher net reproductive rates, and faster mean generation and doubling times. Spodoptera frugiperda larvae reared on 'Maverick', 'Pipeline', and 'UA5414RR' had higher intrinsic and finite rates of increase, higher net reproductive rates, and faster mean generation and doubling times compared to 'Quickpick Pinkeye'. Spodoptera exigua larvae had the highest survivorship on 'Maverick' and similar, positive lifetable statistics when reared on 'Maverick' and 'Pipeline'. The results of this study indicate hemp is an alternative host plant that has the potential to influence the population dynamics of C. includens, S. frugiperda, and S. exigua in Louisiana agroecosystems they co-occur in.

Investigating physical and mechanical properties of nest soils used by mud dauber wasps from a geotechnical engineering perspective.

The quality of nest soils has significant effects on reproductive success in mud dauber species. This study investigated the physical and mechanical properties of the nest soils used by mud daubers from a geotechnical engineering perspective. One hundred thirty-one nests of black and yellow mud daubers were collected from five locations in the south of Louisiana. Moisture and organic contents, densities, void ratios, plasticity, grain size distributions, soil classifications, and penetration resistances of the nest soils were measured. Also, the performance of mud daubers' nest-compaction method (i.e., repetitive tapping produced by the front legs and mandibles) was evaluated by comparing the densities and penetration resistances between mud dauber nests and Proctor compacted nest soil samples. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray diffraction were used to measure the morphology, elemental composition, and mineralogy of the nest soils. Mud dauber nests were made of hard and very stiff well-graded silty soils. The high strengths and high densities of mud dauber nests were attributed to repetitive tapping (similar to vibratory compaction in geotechnical engineering) used by mud daubers for nest construction, high capillary cohesion in the nest soils, well-graded soil grain size distribution, and clay minerals serving as cementing agents in the nest soils.

Surf and turf vision: Patterns and predictors of visual acuity in compound eye evolution.

Eyes have the flexibility to evolve to meet the ecological demands of their users. Relative to camera-type eyes, the fundamental limits of optical diffraction in arthropod compound eyes restrict the ability to resolve fine detail (visual acuity) to much lower degrees. We tested the capacity of several ecological factors to predict arthropod visual acuity, while simultaneously controlling for shared phylogenetic history. In this study, we have generated the most comprehensive review of compound eye visual acuity measurements to date, containing 385 species that span six of the major arthropod classes. An arthropod phylogeny, made custom to this database, was used to develop a phylogenetically-corrected generalized least squares (PGLS) linear model to evaluate four ecological factors predicted to underlie compound eye visual acuity: environmental light intensity, foraging strategy (predator vs. non-predator), horizontal structure of the visual scene, and environmental medium (air vs. water). To account for optical constraints on acuity related to animal size, body length was also included, but this did not show a significant effect in any of our models. Rather, the PGLS analysis revealed that the strongest predictors of compound eye acuity are described by a combination of environmental medium, foraging strategy, and environmental light intensity.

Two new species and distribution records for the genus Bohayella Belokobylskij, 1987 from Costa Rica (Hymenoptera, Braconidae, Cardiochilinae).

Two new species of Bohayella Belokobylskij, 1987 from Costa Rica are described: Bohayella geraldinae Kang, sp. nov. and Bohayella hansoni Kang, sp. nov. These are new distribution records for the genus in the Neotropical region. In addition, a key to species of the genus Bohayella of Costa Rica is presented. The current work elevates the number of species included in Bohayella from nine to eleven.

Orientocardiochiles, a new genus of Cardiochilinae (Hymenoptera, Braconidae), with descriptions of two new species from Malaysia and Vietnam.

For the first time in 21 years, a new genus of cardiochiline braconid wasp, Orientocardiochiles Kang & Long, gen. nov. (type species Orientocardiochiles joeburrowi Kang, sp. nov.), is discovered and described. This genus represents the ninth genus in the Oriental region. Two new species (O. joeburrowi Kang, sp. nov. and O. nigrofasciatus Long, sp. nov.) are described and illustrated, and a key to species of the genus, with detailed images, is added. Diagnostic characters of the new genus are analyzed and compared with several other cardiochiline genera to allow the genus to key out properly using an existing generic treatment. The scientific names validated by this paper and morphological data obtained from this project will be utilized and tested in the upcoming genus-level revision of the subfamily based on combined morphological and molecular data.

Structural Diversity with Varying Disorder Enables the Multicolored Display in the Longhorn Beetle Sulawesiella rafaelae.

Light control through layered photonic nanostructures enables the strikingly colored displays of many beetles, birds, and butterflies. To achieve different reflected colors, natural organisms mainly rely on refractive index variations or scaling of a fixed structure design, as opposed to varying the type of structure. Here, we describe the presence of distinct coloration mechanisms in the longhorn beetle Sulawesiella rafaelae, which exhibits turquoise, yellow-green, and orange colors, each with a variable iridescence. By optical and electron microscopy, we show that the colors originate from multilayered architectures in hair-like scales with varying amounts of structural disorder. Structural characterizations and optical modeling show that the disorder strongly influences the optical properties of the scales, allowing an independent adjustment of the optical response. Our results shed light on the interplay of disorder in multilayered photonic structures and their biological significance, and could potentially inspire new ecological research and the development of novel optical components.

Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles.

Opsin proteins are fundamental components of animal vision whose structure largely determines the sensitivity of visual pigments to different wavelengths of light. Surprisingly little is known about opsin evolution in beetles, even though they are the most species rich animal group on Earth and exhibit considerable variation in visual system sensitivities. We reveal the patterns of opsin evolution across 62 beetle species and relatives. Our results show that the major insect opsin class (SW) that typically confers sensitivity to "blue" wavelengths was lost ~300 million years ago, before the origin of modern beetles. We propose that UV and LW opsin gene duplications have restored the potential for trichromacy (three separate channels for colour vision) in beetles up to 12 times and more specifically, duplications within the UV opsin class have likely led to the restoration of "blue" sensitivity up to 10 times. This finding reveals unexpected plasticity within the insect visual system and highlights its remarkable ability to evolve and adapt to the available light and visual cues present in the environment.