RESUMO
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.
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Museus , Manejo de Espécimes , Animais , História NaturalRESUMO
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.
Assuntos
Columbidae , DNA Mitocondrial , Animais , Columbidae/genética , DNA Mitocondrial/química , DNA Mitocondrial/genética , Variação Genética , Filogenia , FilogeografiaRESUMO
The taxonomically diverse and relatively understudied avifauna of Papua New Guinea's (PNG) island archipelagos provide a unique ecological framework for studying haemosporidian parasite differentiation and geographic structure. We implemented molecular and phylogenetic analyses of partial mitochondrial DNA sequences to assess the host distribution of 3 genera of vector-transmitted avian blood parasites (Plasmodium, Leucocytozoon and Haemoproteus) across a range of islands off the southeastern tip of PNG. We identified 40 new lineages of haemosporidians, including five lineages belonging to Leucocytozoon, a genus not previously described in this region. Leucocytozoon infections were only observed on the larger, human-inhabited islands. Lineages belonging to Haemoproteus were diverse and had broad geographic distribution. Compared to the mainland, Haemoproteus parasites on the smaller, more distant islands had greater host specificity and lower infection prevalence. The black sunbird (Leptocoma aspasia), a commonly caught species, was shown to be a rare host for Haemoproteus spp. infections. Moreover, although birds of the genus Pitohui harbor a neurotoxin (homobatrachotoxin), they demonstrated an infection prevalence comparable to other bird species. The islands of PNG display heterogeneous patterns of haemosporidian diversity, distribution and host-specificity and serve as a valuable model system for studying host-parasite-vector interactions.
Assuntos
Doenças das Aves , Haemosporida , Parasitos , Passeriformes , Plasmodium , Infecções Protozoárias em Animais , Animais , Baías , Doenças das Aves/epidemiologia , Doenças das Aves/parasitologia , Haemosporida/genética , Humanos , Papua Nova Guiné/epidemiologia , Parasitos/genética , Filogenia , Plasmodium/genética , Prevalência , Infecções Protozoárias em Animais/epidemiologia , Infecções Protozoárias em Animais/parasitologiaRESUMO
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high-elevation and low-elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modelling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that although in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.
Assuntos
Altitude , Aves/genética , Fluxo Gênico , Especiação Genética , Animais , Nova Guiné , FilogeografiaRESUMO
Giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon), also known as giant elephant-shrews, are small-bodied mammals that range from central through eastern Africa. Previous research on giant sengi systematics has relied primarily on pelage color and geographic distribution. Because some species have complex phenotypic variation and large geographic ranges, we used molecular markers to evaluate the phylogeny and taxonomy of the genus, which currently includes four species: R. chrysopygus, R. cirnei (six subspecies), R. petersi (two subspecies), and R. udzungwensis. We extracted DNA from fresh and historical museum samples from all taxa except one R. cirnei subspecies, and we generated and analyzed approximately 4700 aligned nucleotides (2685 bases of mitochondrial DNA and 2019 bases of nuclear DNA) to reconstruct a molecular phylogeny. We genetically evaluate Rhynchocyon spp. sequences previously published on GenBank, propose that the captive R. petersi population in North American zoos is likely R. p. adersi, and suggest that hybridization among taxa is not widespread in Rhynchocyon. The DNA sample we have from the distinctive but undescribed giant sengi from the Boni forest of northern coastal Kenya is unexpectedly nearly identical to R. chrysopygus, which will require further study. Our analyses support the current morphology-based taxonomy, with each recognized species forming a monophyletic clade, but we propose elevating R. c. stuhlmanni to a full species.
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Filogenia , Musaranhos/classificação , Musaranhos/genética , Alelos , Animais , Sequência de Bases , Teorema de Bayes , DNA Mitocondrial/genética , Geografia , Quênia , Pigmentação , Especificidade da EspécieRESUMO
"Supertramp" species are highly specialized overwater dispersers, and are useful taxa for investigating the influence of dispersal ability on speciation and diversification in island settings. The Louisiade White-eye (Zosterops griseotinctus) is a widespread avian supertramp endemic to Papua New Guinea's offshore islands. We used maximum likelihood and Bayesian inference to reconstruct phylogenetic relationships based on 2 mitochondrial and 1 nuclear loci (1813 bp total) from 88 individuals representing all 4 named subspecies and the full breadth of the species' range. We found significant geographic and population genetic structure, and support for a major clade containing the coral islets of the central Louisiade Archipelago and outlying Nissan Island. We found evidence of metapopulation structure and gene flow within the Louisiade Archipelago clade, and relatively high genetic distinctiveness of outlying island populations, including the population on volcanically-defaunated Long Island. We reject a hypothesis of panmixia within the Louisiade White-eye despite their long-range dispersal ability, and find evidence of selection against dispersal ability in populations on high-elevation islands where disturbance is rare. Our study represents a rare intraspecies phylogeny of an avian supertramp, and sheds light on patterns of evolution in highly vagile island species.
Assuntos
Deriva Genética , Passeriformes/genética , Passeriformes/fisiologia , Filogenia , Animais , Teorema de Bayes , Núcleo Celular/genética , DNA Mitocondrial/genética , Evolução Molecular , Fluxo Gênico , Especiação Genética , Papua Nova Guiné , Passeriformes/classificação , FilogeografiaRESUMO
The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at â¼1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.
Assuntos
Migração Animal/fisiologia , Aves Canoras/classificação , Alelos , Animais , Citocromos b/classificação , Citocromos b/genética , DNA Mitocondrial/química , DNA Mitocondrial/genética , DNA Mitocondrial/metabolismo , Variação Genética , Haplótipos , Mitocôndrias/enzimologia , Mitocôndrias/metabolismo , NADH Desidrogenase/classificação , NADH Desidrogenase/genética , América do Norte , Filogenia , Filogeografia , Análise de Sequência de DNA , Aves Canoras/genética , América do SulRESUMO
Birds in the genus Pitohui and Ifrita carry potent neurotoxins that are most abundant in skin and feathers. It was unknown precisely how or where in the skin these chemicals are stored. Here, we report high-resolution electron microscopy using OsO4 staining to visualize the location of alkaloids. Our images suggest that toxic alkaloids accumulate in multigranular bodies of epidermal cells and are likely secreted as part of the avian epidermal barrier, where they are made available for chemical defense.
Assuntos
Alcaloides/metabolismo , Evolução Biológica , Epiderme/metabolismo , Neurotoxinas/metabolismo , Passeriformes/fisiologia , Animais , Epiderme/ultraestrutura , Microscopia Eletrônica de TransmissãoRESUMO
Incredibly powerful whole genome studies of conservation genetics, evolution, and biogeography become possible for non-model organisms when reference genomes are available. Here, we report the sequence and assembly of the whole genome of the little vermilion flycatcher (Pyrocephalus nanus; family Tyrannidae), which is an endemic, endangered, and declining species of the Galapagos Islands. Using PacBio HiFi reads to assemble long contigs and Hi-C reads for scaffolding, we assembled a genome of 1.07â Gb comprising 267 contigs in 152 scaffolds, scaffold N50 74â M, contig N50 17.8â M, with 98.9% assigned to candidate chromosomal sequences and 99.72% of the BUSCO passeriformes 10,844 single-copy orthologs present. In addition, we used the novel HiFiMiTie pipeline to fully assemble and verify all portions of the mitochondrial genome from HiFi reads, obtaining a mitogenome of 17,151 bases, containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, two control regions, and a unique structure of control region duplication and repeats. These genomes will be a critical tool for much-needed studies of phylogenetics, population genetics, biogeography, and conservation genetics of Pyrocephalus and related genera. This genome and other studies that use it will be able to provide recommendations for conservation management, taxonomic improvement, and to understand the evolution and diversification of this genus within the Galapagos Islands.
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Espécies em Perigo de Extinção , Genoma Mitocondrial , Animais , Aves Canoras/genética , Equador , Filogenia , Genoma , Conservação dos Recursos NaturaisRESUMO
The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.
Assuntos
Passeriformes , Animais , Passeriformes/genética , Nova Guiné , Especificidade da Espécie , Filogenia , Ecossistema , Genética Populacional , Filogeografia , GenomaRESUMO
Over the last four decades, Barred Owls (Strix varia) have expanded their range to include much of western North America, including California. This expansion is suspected to have contributed to declining populations of a closely related species, the federally threatened Northern Spotted Owl (Strix occidentalis caurina). As a result, understanding potential health threats to Barred Owls has implications for Spotted Owl health and recovery. From 2016 to 2020, 69 Barred Owls were collected to determine the apparent prevalence of periorbital nematode infection, to identify the parasite species present, and to investigate the potential pathologic effects on their hosts. The nematodes were morphologically identified as Oxyspirura and Aprocta spp. On the basis of phylogenetic analyses, they were clearly divergent from published sequences of other species within these genera. Overall, 34 (49%) Barred Owls were infected with periorbital nematodes, with Oxyspirura sp. infections being much more common (94%) than Aprocta sp. (18%). Histopathology revealed varying severity of conjunctivitis in infected owls. Despite the frequency of infection and subsequent inflammation, parasite burden was not associated with reduced body weight in these owls. As a result, the potential health effect of these nematodes is unclear. Further taxonomic characterization is needed to determine potential novelty of these nematodes.
Assuntos
Nematoides , Estrigiformes , Animais , Filogenia , Prevalência , California/epidemiologiaRESUMO
Spotted owls (SOs, 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) has been listed as "threatened" under the Endangered Species Act since 1990. Here, we use an updated SO genome assembly along with 51 high-coverage whole-genome sequences to examine population structure, hybridization, and recent changes in population size in SO and BO. We found that potential hybrids identified from intermediate plumage morphology were a mixture of pure BO, F1 hybrids, and F1 × BO backcrosses. Also, although SO underwent a population bottleneck around the time of the Pleistocene-Holocene transition, their population sizes rebounded and show no evidence of any historical (i.e., 100-10,000 years ago) population decline. This suggests that the current decrease in SO abundance is due to events in the past century. Finally, we estimate that western and eastern BOs have been genetically separated for thousands of years, instead of the previously assumed recent (i.e., <150 years) divergence. Although this result is surprising, it is unclear where the ancestors of western BO lived after the separation. In particular, although BO may have colonized western North America much earlier than the first recorded observations, it is also possible that the estimated divergence time reflects unsampled BO population structure within central or eastern North America.
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Variação Genética , Estrigiformes/classificação , Estrigiformes/genética , Animais , Quimera , Plumas , Feminino , Genética Populacional , Genoma , Masculino , Fenótipo , Dinâmica Populacional , Estados UnidosRESUMO
Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (NaV) function. Among these, batrachotoxin (BTX) from Pitohui poison birds and Phyllobates poison frogs stands out because of its lethality and unusual effects on NaV function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore-forming helix N-to-T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost compromising channel function, and fails to produce BTX-resistant channels in poison frog NaVs. We also show that captivity-raised poison frogs are resistant to two NaV-directed toxins, BTX and saxitoxin (STX), even though they bear NaVs sensitive to both. Moreover, we demonstrate that the amphibian STX "toxin sponge" protein saxiphilin is able to protect and rescue NaVs from block by STX. Taken together, our data contradict the hypothesis that BTX autoresistance is rooted in the DIVS6 NâT mutation, challenge the idea that ion channel mutations are a primary driver of toxin resistance, and suggest the possibility that toxin sequestration mechanisms may be key for protecting poisonous species from the action of small-molecule toxins.
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Venenos , Animais , Batraquiotoxinas , Aves , Mutação , Venenos/toxicidade , Canais de Sódio/genéticaRESUMO
The human-caused extinction of the Passenger Pigeon (Ectopistes migratorius) is one of the best known and documented of any bird. This event was particularly alarming because the Passenger Pigeon went from being one of the most numerous avian species in the world to extinct in a period of decades, when the last individual died in captivity in a Cincinnati Zoo in 1914. While a great deal of information exists on the likely direct and indirect causes of its demise, as well as information on life-history, the phylogenetic relationships of this species have been subject to considerable speculation. Here we use DNA sequences obtained from museum specimens to resolve the phylogenetic position of this species with respect to other pigeons and doves (Columbiformes). We show that the Passenger Pigeon is not related to the New World mourning doves (Zenaida) as many authors have suggested, but is the sister taxon of all other New World pigeons (Patagioenas). Biogeographic analysis suggests the Passenger Pigeon lineage may have colonized North America from Asia, and subsequently dispersed into South America, leading to a more extensive radiation of New World pigeons.
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Columbidae/classificação , Columbidae/genética , Extinção Biológica , Filogenia , Animais , Núcleo Celular/genética , DNA Mitocondrial/genética , Geografia , Análise de Sequência de DNARESUMO
Bird species in the avian genus Pitohui contain potent neurotoxic alkaloids that may be used for defense. The genus comprises multiple species that are endemic to New Guinea and were presumed to belong to the family Pachycephalidae or Colluricinclidae, within the core corvoidea, an ancient Australasian radiation of crow-like birds. In order to understand the evolution of toxicity within the genus Pitohui, we sequenced three mitochondrial and two nuclear gene segments and reconstructed a phylogeny of the genus Pitohui and its putative relatives. We show that the genus Pitohui is polyphyletic, and consists of five different lineages. Using Bayesian ancestral state reconstruction, we estimate that toxicity likely evolved multiple times within this group. Furthermore, because the morphological and behavioral similarity among these poisonous birds appears to have evolved convergently, we hypothesize that this may be a possible example of Müllerian mimicry in birds. The Morningbird of Palau, Micronesia, that has often been included in the genus Pitohui, actually belongs in the genus Pachycephala and offers an intriguing case of pronounced evolution on a remote oceanic island.
Assuntos
Evolução Molecular , Neurotoxinas/genética , Passeriformes/genética , Filogenia , Animais , Teorema de Bayes , DNA Mitocondrial/genética , Plumas , Genes Mitocondriais , Funções Verossimilhança , Cadeias de Markov , Mitocôndrias/genética , Método de Monte Carlo , Nova Guiné , Palau , Passeriformes/classificação , Pigmentação , Alinhamento de Sequência , Análise de Sequência de DNARESUMO
As the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix varia and S. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of western S. varia that suggested admixture with S. occidentalis appear unrelated to S. occidentalis ancestry and may instead reflect local selection.
Assuntos
Genoma , Análise de Sequência de DNA , Estrigiformes/genética , Animais , Estudo de Associação Genômica Ampla , América do Norte , Especificidade da EspécieRESUMO
Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.
RESUMO
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100-375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226-19,522 nt in length and included copies of all mitochondrial genes except tRNAPro , ND6, and tRNAGlu . Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.
RESUMO
We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from â¼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.