Birds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed datasets of pattern phenotypes that were heretofore inaccessible. In this review, we synthesize recent and classic studies of plumage patterns at different evolutionary and organismal scales and discuss the various roles that plumage patterns play in avian biology. We dissect the role of plumage patches as signals within and among species. We also consider the evolutionary history of plumage patterns, including phylogenetic comparative studies and evolutionary developmental research of the genetic architecture underlying plumage patterns. We also survey an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches. Finally, we provide a worked example to illustrate a potential workflow with dorsal plumage patterns among subspecies of the Horned Lark (Eremophila alpestris) in western North America. Studies of plumage patterning and coloration have played a prominent role in ornithology thus far, and recent methodological and conceptual advances have opened new avenues of research on the ecological functions and evolutionary origins of plumage patterns in birds.LAY SUMMARYBirds have many different plumage patterns that arise from coloration motifs within feathers as well as differences in color among body regions.Plumage patterns play various roles in bird biology. They are involved in mate choice and territoriality, social interactions, camouflage from predators, and many other functions.There is a rich history of detailed study on plumage patterns, which we review and synthesize in this manuscript.Recent advances in photography and image processing algorithms have opened new avenues of research on plumage patterns. These open-source methods enable efficient, repeatable, and scalable analytical pipelines.We illustrate one possible pipeline with a worked example of geographic variation in dorsal plumage patterns among populations of Horned Lark (Eremophila alpestris) in the western United States.Looking ahead, enhanced capacity and scalability for digital photography analyses will reveal new discoveries regarding the ecology and evolution of avian plumage patterns.

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Plumage patterns: Ecological functions, evolutionary origins, and advances in quantification

Strong cultural heritage management relies on a thorough evaluation of the threats faced by heritage sites, both in the present and in the future. In this study, we analysed the changes in the position of Hiorthhamn shoreline (Svalbard), which is affecting coastal cultural heritage sites, for a period of 93 years (1927–2020). Shoreline changes were mapped by using maps, ortophotos, drone images, terrestrial laser scanning (TLS), and topographic surveys. Also, TLS was used to 3D document the endangered coastal cultural heritage sites. Detailed sedimentological and morphological mapping was made in the field and from the newly acquired drone images in order to understand shoreline-landscape interaction and to depict changes occurring from 2019 to 2020. Short-term (2019–2020) and long-term (1927–2020) shoreline erosion/accretion was made with the help of the Digital Shoreline Analysis System (DSAS) and prompted a subdivision of three sectors, based on change pattern. Compared to a previous long-term analysis (1927–2019), this year’s average erosion rate analysis (expressed by the EPR parameter) for the 93-year period is −0.14 m/yr. This shift in mean development is due to a newly formed spit-bar in Sector 2. Referring strictly to Sector 1, where the protected cultural heritage objects are located, the erosion rate increased from the previous analysis of –0.76 m/yr to −0.77 m/yr. The shoreline forecast analysis highlights that half of the protected cultural heritage objects will likely disappear over the next decade and almost all the cultural heritage objects analysed in this study will disappear in roughly two decades. This shows the great danger the Arctic’s cultural heritage sites is in if no mitigation measures are undertaken by the local authorities.

https://www.mdpi.com/2073-4441/13/6/784/pdf

Coastal Erosion of Arctic Cultural Heritage in Danger: A Case Study from Svalbard, Norway

Digital 3D modelling and visualization technologies have been widely applied to support research in the humanities since the 1980s. Since technological backgrounds, project opportunities, and methodological considerations for application are widely discussed in the literature, one of the next tasks is to validate these techniques within a wider scientific community and establish them in the culture of academic disciplines. This article resulted from a postdoctoral thesis and is intended to provide a comprehensive overview on the use of digital 3D technologies in the humanities with regards to (1) scenarios, user communities, and epistemic challenges; (2) technologies, UX design, and workflows; and (3) framework conditions as legislation, infrastructures, and teaching programs. Although the results are of relevance for 3D modelling in all humanities disciplines, the focus of our studies is on modelling of past architectural and cultural landscape objects via interpretative 3D reconstruction methods.

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Digital 3D Technologies for Humanities Research and Education: An Overview

Describing a substantial proportion of the world’s species could be made much easier by the 3D digitization of collections, which would facilitate the dissemination of taxonomic information locked up in natural history museums. Three-dimensional imaging captures many characters and allows a lot of versatility in the way that morphological data is displayed and used (Wheeler et al. 2012; Faulwetter et al. 2013). Moreover, the loss and damage of valuable specimens, many of which are very fragile, can be reduced as a result of the use and sharing of 3D model substitutes among researchers. This can also lead to a reduction in the handling and transportation expenses of many specimens.

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Virtual Equivalents of Real Objects (VEROs): A type of non-fungible token (NFT) that can help fund the 3D digitization of natural history collections

https://onlinelibrary.wiley.com/doi/pdf/10.1111/cura.12423

Museum Leadership for Engaging, Equitable Education: The Transformative Potential of Digitized Collections for Authentic Learning Experiences

Natural history collections are yielding more information as digitization brings specimen data to researchers, connects specimens across museums, and as new technologies allow for more large-scale data collection. Therefore, a key goal in specimen digitization is developing methods that both increase access and allow for the highest yield of phenomic data. 3D digitization is increasingly popular because it has the potential to meet both aspects of that key goal. However, current methods overlook or do not prioritize some of the most sought-after phenotypic traits, those involving the external appearance of specimens, especially color. Here, we introduce an efficient and cost-effective pipeline for 3D photogrammetry to capture the external appearance of natural history specimens and other museum objects. 3D photogrammetry aligns and compares sets of dozens, hundreds, or even thousands of photos to create 3D models. The hardware set-up requires little physical space and around $3,000 in initial investment, while the software pipeline requires $1,400/year for proprietary software subscriptions (with open-source alternatives). The creation of each 3D model takes 1-2 hours/specimen and much of the software pipeline is automated with minimal supervision required, including the onerous step of mesh processing. We showcase the method by creating 3D models for most of the type specimens in the Moore Laboratory of Zoology bird collection and show that digital bill measurements are comparable to hand-taken measurements. Color data, while not included as part of this pipeline, is easily extractable from the models and one of the most promising areas of data collection. Future advances can adapt the method for ultraviolet reflectance capture and increased efficiency and model quality. Combined with genomic data, phenomic data from 3D models including photogrammetry will open new doors to understanding organismal evolution.

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A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry.

Hybridization involving introduced species is becoming more common as humans modify landscapes and ecosystems. When two closely related species are introduced to the same area, their niche dynamics will dictate the level of sympatry and potential for hybridization. Amazona parrots offer a rare case where multiple closely related species have established as breeders in Southern California. Red-crowned Parrots (A. viridigenalis) and Lilac-crowned Parrots (A. finschi) are particularly interesting because they are sister species with allopatric native ranges in Mexico. In Southern California, where they established in the 1980s and have since grown in numbers, they appear to occupy the same urban habitat. We sought to test whether introduced Red-crowned and Lilac-crowned parrots have shifted their niches compared to their native ranges, and if so, whether sympatry has led to hybridization. Using broad-scale environmental data collected from weather stations and orbiting satellites, we found that Red- crowned and Lilac-crowned parrots have partially divergent environmental niches in their native ranges, but now occupy the same environmental niche in their introduced range in Southern California. This new niche is largely different from what they experience in their respective home ranges, supporting a niche- shift model of species introduction. Due to this niche shift, the two species now come into contact across Southern California, leading to hybridization. Genomic markers support the existence of some recent hybrids as well as advanced backcrosses resulting from older hybridization events closer to the time of first introduction. Photographs from community scientists included as part of the Free-flying Los Angeles Parrot Project (FLAPP) also document hybrids, but underestimate their frequency compared to genetic data. Despite evidence for ongoing hybridization, the bimodal distribution of ancestry among the introduced population points to the existence of reproductive isolating mechanisms keeping the two species distinct. Further study is needed to understand if reproductive isolating mechanisms result from behavioral factors, such as conspecific flocking preferences, suggested by the community science data, or from genomic incompatibilities built up from a long history of isolation in Mexico. The integrity of these genetic lineages in Southern California carries important conservation implications, as both species are listed as endangered in their native ranges due to trapping for the pet trade and habitat loss.

/pdf/niche-shifts-and-hybridization-in-two-amazona-parrot-sister-4ae9m2ahpa.pdf

Niche shifts and hybridization in two Amazona parrot sister-species introduced to Southern California

This paper has been withdrawn by the authors while evaluating reviewer concerns about interpretation of the genomic data and due to errors found by the authors in the scoring of photos. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.

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Siddharth Sannapareddy

Papers

A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry.

Niche shifts and hybridization in two Amazona parrot sister-species introduced to Southern California

Niche shifts lead to hybridization between two Amazona parrot sister-species introduced to Southern California