Rauri C K Bowie

University of California, Berkeley | UCB · Department of Integrative Biology

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Convergent evolution is widely regarded as a signature of adaptation. However, testing the adaptive consequences of convergent phenotypes is challenging, making it difficult to exclude non-adaptive explanations for convergence. Here, we combined feather reflectance spectra and phenotypic trajectory analyses with visual and thermoregulatory modellin...

Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source of assembly gaps. This makes it difficult to decipher the impact of these elements on the dynamics of genome evolution. The increased capacity of long-read sequencing technologies to span highly repeti...

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoreg...

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechan...

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds total...

Thermal soaring conditions above the sea have long been assumed absent or too weak for terrestrial migrating birds, forcing large obligate soarers to take long detours and avoid sea crossing, and facultative soarers to cross exclusively by costly flapping flight. Thus, while atmospheric convection does develop at sea and is utilized by some seabird...

Both frugivores and nectarivores are potentially exposed to dietary ethanol produced by fermentative yeasts which metabolize sugars. Some nectarivorous mammals exhibit a preference for low-concentration ethanol solutions compared to controls of comparable caloric content, but behavioural responses to ethanol by nectar-feeding birds are unknown. We...

Whole-genome level comparisons of sister taxa that vary in phenotype against a background of high genomic similarity can be used to identify the genomic regions that might underlie their phenotypic differences. In wild birds, this exploratory approach has detected markers associated with plumage coloration, beak and wing morphology, and complex beh...

The Eastern Arc Mountains of Tanzania and Kenya, a montane archipelago of 13 uplifted fault blocks (sky islands) isolated by lowland arid savanna, are a center of exceptional biological endemism. Under the influence of humid winds from the Indian Ocean, forests and associated species may have persisted in this region since the final uplift of these...

The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP...

Background Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for...

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into t...

To avoid the worst outcomes of the current biodiversity crisis we need a deep understanding of population responses to human-induced ecological change. Rapidly expanding access to genomic resources for non-model taxa promises to play a unique role in meeting this goal. In particular, the increasing feasibility of sequencing DNA from historical spec...

To avoid the worst outcomes of the current biodiversity crisis we need a deep understanding of population responses to human-induced ecological change. Rapidly expanding access to genomic resources for non-model taxa promises to play a unique role in meeting this goal. In particular, the increasing feasibility of sequencing DNA from historical spec...

The relationship between ecology and morphology is a cornerstone of evolutionary biology, and quantifying variation across environments can shed light on processes that give rise to biodiversity. Three morphotypes of the Steller's Jay (Cyanocitta stelleri) occupy different ecoregions in western North America, which vary in climate and landcover. Th...

Migration is one of the most physical and energetically demanding periods in an individual bird’s life. The composition of the bird’s gut or cloacal microbiota can temporarily change during migration, likely due to differences in diets, habitats and other environmental conditions experienced en route. However, how physiological condition, migratory...

We present a perspective which supports the findings of recent research proposing changes to the taxonomy of francolins and spurfowls.

Animal coloration serves many biological functions and must therefore balance potentially competing selective pressures. For example, many animals have camouflage in which coloration matches the visual background that predators scan for prey. However, different colors reflect different amounts of solar radiation and may therefore have thermoregulat...

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for fecal microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at t...

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as “fieldwork.” Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of t...

Twenty years after establishing the genus Amblymelanoplia Dombrow, 2002 a large amount of new material collected has warranted a critical review of the established species and a revision of the genus. From this process, we describe 93 new species from the Northern Cape, Western Cape, Mpumalanga and Limpopo Provinces of the Republic of South Africa....

Insights into the processes underpinning the evolution of phenotypic parallelism contribute to our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgr...

Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. To this end, museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure....

Avian influenza viruses (AIV) are a worldwide threat to animal and human health. As wild waterfowl circulate and spread these viruses around the world, investigations of AIV prevalence in wild populations are critical for understanding pathogen transmission, as well as predicting disease outbreaks in domestic animals and humans. Surveillance effort...

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as “fieldwork.” Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of t...

Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the m...

The cover image is based on the Letter AVONET: morphological, ecological and geographical data for all birds by Tobias et al., https://doi.org/10.1111/ele.13898. The sword‐billed hummingbird (Ensifera ensifera) is exquisitely adapted to its trophic niche as an aerial pollinator of flowerings plants (angiosperms) in the high Andes. A new global data...

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVON...

In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at the sam...

Background: Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for...

Genetic structure and phenotypic variation among populations is affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gra...

Aizoaceae (Caryophyllales) constitute one of the major floral components of the unique Greater Cape Floristic Region (GCFR), with more than 1700 species and 70% endemism. Within succulent Aizoaceae, the subfamily Ruschioideae is the most speciose and rapidly diversifying clade, offering potential niches for the diversification of specialized herbiv...

Africa’s montane areas are broken up into several large and small units, each isolated as forest-capped “sky islands” in a “sea” of dry lowland savanna. Many elements of their biota, including montane forest birds, are shared across several disjunct mountains, yet it has been difficult to rigorously define an Afromontane forest avifauna, or determi...

Learned traits are thought to be subject to different evolutionary dynamics than other phenotypes, but their evolutionary tempo and mode has received little attention. Learned bird song has been thought to be subject to rapid and constant evolution. However, we know little about the evolutionary modes of learned song divergence over long timescales...

Response to the article by Hunter et al. about the recent review of the taxonomy of francolins and spurfowls.

Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pat...

Aim Delimiting recently diverged species is challenging. During speciation, genetic differentiation may be distributed unevenly across the genome, as different genomic regions can be subject to different selective pressures and evolutionary histories. Reliance on limited numbers of genetic markers that may be underpowered can make species delimitat...

Southern Africa is remarkably rich in avian species diversity; however, the evolutionary and biogeographic mechanisms responsible for that diversity are, in general, poorly understood, and this is particularly true with respect to the many species that are endemic or near-endemic to the region. Here, we used mtDNA to assess genetic structure in thr...

Migration is the primary strategy that temperate birds use to avoid overwintering under harsh conditions. As a consequence, migratory birds have evolved specific morphological features in their wings and skeleton. However, in addition to varying in overall shape and size, bone can also change at the microstructural level by, for example, increasing...

Animal coloration serves many biological functions and must therefore balance potentially competing selective pressures. For example, many animals have camouflage, in which coloration matches the visual background against which predators scan for prey. However, different colors reflect different amounts of solar radiation and may therefore have the...

Human activities shape resources available to wild animals, impacting diet and likely altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS‐tracking) over three periods of their migratory cycle,...

The presence of two undescribed cisticola warblers in the marshes of the Kilombero floodplain in central Tanzania has been known since the 1980s and these putative new species have been illustrated in field guides on African birds, although with no formal name. Here we name both species, based on two museum specimens collected in 1961 and recently...

The review by Hunter et al. (2021) on the delineation of certain francolin and spurfowl taxa as full species by Mandiwana-Neudani et al. (2019a, 2019b) appears to be largely orientated around their application of the Biological Species Concept (BSC). We employed an integrative taxonomy framework, evaluating morphological characters from across each...

Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.¹ During the latter half of the twentieth century, North America’s largest soaring bird,² the California condor (Gymnogyps californianus; Critically Endanger...

Species delimitation requires a broad assessment of population-level variation using multiple lines of evidence, a process known as integrative taxonomy. More specifically, studies of species limits must address underlying questions of what limits the distribution of populations, how traits vary in association with different environments, and wheth...

Spotted owls (SO, Strix occidentalis) are a flagship species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (S. o. caurina)...

Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geogra...

Natural history collections provide an unparalleled resource for documenting population responses to past anthropogenic change. However, in many cases, traits measured on specimens may vary temporally in response to a number of different anthropogenic pressures or demographic processes. While teasing apart these different drivers is challenging, ap...

Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gu...

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...

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruc...

Few studies have quantified the extent of genetic differentiation within widely distributed polytypic African bird species with disjunct ranges. Current knowledge indicates that high levels of genetic differentiation are found for such lineages but generalisation of the pattern requires further comparisons with other co‐distributed taxa. We assesse...

Hermit Warblers (Setophaga occidentalis) sing a formulaic, type I song to attract mates, in contrast to a repertoire of more complex, type II songs to defend territories. A single, dominant type I song, or a low diversity of type I songs, often occur within a geographic area. We provide the first comprehensive description of Hermit Warbler type I s...

Aim The conservation of biodiversity is hampered by data deficiencies, with many new species and subspecies awaiting description or reclassification. Population genomics and ecological niche modelling offer complementary new tools for uncovering functional units of phylogenetic diversity. We hypothesize that phylogenetically delineated lineages of...

We provide an addendum vis-à-vis Mandiwana-Neudani et al. (2019a) on the taxonomy, phylogeny and biogeography of ‘true’ francolins: Galliformes, Phasianidae, Phasianinae, Gallini; Francolinus, Ortygornis, Afrocolinus gen. nov., Peliperdix and Scleroptila spp., Mandiwana-Neudani et al. (2019b). Mandiwana-Neudani et al. (2019a) proposed the use of a...

Gut microbial diversity is thought to reflect the co‐evolution of microbes and their hosts as well as current host‐specific attributes such as genetic background and environmental setting. To explore interactions among these parameters, we characterized variation in gut microbiome composition in California voles (Microtus californicus) across a con...

Environments are heterogeneous in space and time, and the permeability of landscape and climatic barriers to gene flow may change over time. When barriers are present, they may start populations down the path toward speciation, but if they become permeable before the process of speciation is complete, populations may once more merge. In Southern Af...

The behavioral ecology of host species is likely to affect their microbial communities, because host sex, diet, physiology, and movement behavior could all potentially influence their microbiota. We studied a wild population of barn owls (Tyto alba) and collected data on their microbiota, movement, diet, size, coloration, and reproduction. The comp...

Spotted owls (SO, Strix occidentalis) are a keystone species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (subspecies S....

Phenotypic plasticity has the potential to influence environmental adaptation on extremely short evolutionary timescales. Transgenerational plasticity (TGP) allows parents to provision their offspring for rapid environmental shifts in as little as one generation. We hypothesized that organisms that produce multiple generations of offspring each yea...

Signals used in animal communication, especially those that are learned, are thought to be prone to rapid and/or regular evolution. It has been hypothesized that the evolution of song learning in birds has resulted in elevated diversification rates, as learned song may be subject to especially rapid evolution, and song is involved in mate choice. H...

Afro-Asiatic perdicine galliform taxa commonly and inconsistently referred to as francolins, spurfowls and partridges have contentious taxonomic and phylogenetic histories. Hall combined two putative monophyletic, but taxonomically unnamed, clades comprising 28 perdicine species known as ‘francolins’ or fisante in South Africa and 13 more quail-lik...

We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler ( Oreothlypis celata ) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the...

The study of systematics in wide-ranging seabirds can be challenging due to the vast geographic scales involved, as well as the possible discordance between molecular, morphological and behavioral data. In the Southern Ocean, macaroni penguins (Eudyptes chrysolophus) are distributed over a circumpolar range including populations in Antarctic and su...

The implementation of intelligent software to identify and classify objects and individuals in visual fields is a technology of growing importance to operatives in many fields, including wildlife conservation and management. To non-experts, the methods can be abstruse and the results mystifying. Here, in the context of applying cutting edge methods...