Species identification of birds through genetic analysis of naturally shed feathers

Genetic analysis of noninvasively collected bird feathers is of growing importance to avian ecology; however, most genetic studies that utilize feathers make no mention of the need to verify their species of origin. While plumage patterns and collection location often are indicative of species identity, broad‐scale feather collections may require definitive species identification prior to analysis. Genetic species identification has been applied to noninvasively collected samples from a wide range of taxa but, to date, these techniques have not been widely used on bird feathers. Here, we develop and test a polymerase chain reaction (PCR)‐based technique for identifying eastern imperial eagle (Aquila heliaca) samples among a vast number of noninvasively collected feathers. Species identification is accomplished by amplifying a fragment of the mitochondrial cytochrome c oxidase I gene, then digesting that fragment with a restriction enzyme. The resulting species‐specific restriction fragment length polymorphisms (RFLPs) are easily visualized by gel electrophoresis. We tested this PCR‐RFLP assay on over 300 individuals that had been genetically identified from noninvasively collected feathers and demonstrated that the assay is both reliable and robust for DNA of low quality and quantity. The genetic methods of species identification used to develop this assay can readily be applied to other bird assemblages, making them particularly relevant to a broad range of future avian research.     

The reliability of pigment pattern‐based identification of wild bottlenose dolphins

Long‐term studies often rely on natural markings for individual identification across time. The primary method for identification in small cetaceans relies on dorsal fin shape, scars, and other natural markings. However, dorsal fin markings can vary substantially over time and the dorsal fin can become unrecognizable after an encounter with a boat or shark. Although dorsal fins have the advantage in that they always break the water surface when the cetacean breathes, other physical features, such as body scars and pigmentation patterns can supplement. The goal of this study was to explore the use of dorso‐lateral pigment patterns to identify wild bottlenose dolphins. We employed photographic pigment matching tests to determine if pigmentation patterns showed (1) longitudinal consistency and (2) bilateral symmetry using a 30 yr photographic database of bottlenose dolphins (Tursiops aduncus). We compared experienced dolphin researchers and inexperienced undergraduate student subjects in their ability to accurately match images. Both experienced and inexperienced subjects correctly matched dolphin individuals at a rate significantly above chance, even though they only had 10 s to make the match. These results demonstrate that pigment patterns can be used to reliably identify individual wild bottlenose dolphins, and likely other small cetacean species at other sites.     

A non-invasive genetic evaluation of population size,natal philopatry,and roosting behavior of non-breeding eastern imperial eagles (<Emphasis Type="Italic">Aquila heliaca</Emphasis>) in central Asia

Roughly one-third of all eagle species are considered to be threatened or endangered, but the ecology of most eagles remains poorly understood. While the pronounced territoriality of breeding adults facilitates behavioral studies, the demography of non-breeding individuals (pre-adults and non-territorial floaters) is almost completely unknown. Traditionally, limited data on pre-adult and floater movement come from wing-tagging and/or telemetry studies. As an alternative to these methods we used genetic analyses of non-invasively collected feathers to investigate the population biology of non-breeding eastern imperial eagles (Aquila heliaca) in Kazakhstan. Microsatellite profiles of shed feathers indicate that eastern imperial eagles roost communally with other raptors. Furthermore, roosts are large and dynamic: 287 non-breeding eastern imperial eagles were detected in our sample, and a mark-recapture analysis estimated the total number to be 308 ± 8. The natal origins of these individuals were investigated by comparing their microsatellite profiles to those available for >90% of the eastern imperial eagle chicks hatched at the study site over the six previous breeding seasons. Only 4% of the individuals genetically matched a chick, suggesting that the reserve may serve as a critical refugium for pre-adults and itinerant floaters. Feathers have long been recognized as a suitable source of DNA, but few studies have used wide-scale, non-invasive collections of feathers (>1,000 samples) to investigate fundamental aspects of avian biology. Our research demonstrates that non-invasive genetic analyses of feathers can be used to evaluate population size, natal philopatry, and local movements of birds that are difficult to study using traditional means.     

Mechanical and structural adaptations to migration in the flight feathers of a Palaearctic passerine

Current avian migration patterns in temperate regions have been developed during the glacial retreat and subsequent colonization of the ice‐free areas during the Holocene. This process resulted in a geographic gradient of greater seasonality as latitude increased that favoured migration‐related morphological and physiological (co)adaptations. Most evidence of avian morphological adaptations to migration comes from the analysis of variation in the length and shape of the wings, but the existence of intra‐feather structural adjustments has been greatly overlooked despite their potential to be under natural selection. To shed some light on this question, we used data from European robins Erithacus rubecula overwintering in Campo de Gibraltar (Southern Iberia), where sedentary robins coexist during winter with conspecifics showing a broad range of breeding origins and, hence, migration distances. We explicitly explored how wing length and shape, as well as several functional (bending stiffness), developmental (feather growth rate) and structural (size and complexity of feather components) characteristics of flight feathers, varied in relation to migration distance, which was estimated from the hydrogen stable isotope ratios of the summer‐produced tail feathers. Our results revealed that migration distance not only favoured longer and more concave wings, but also promoted primaries with a thicker dorsoventral rachis and shorter barb lengths, which, in turn, conferred more bending stiffness to these feathers. We suggest that these intra‐feather structural adjustments could be an additional, largely unnoticed, adaptation within the avian migratory syndrome that might have the potential to evolve relatively quickly to facilitate the occupation of seasonal environments.     

White tail spots in breeding Barn Swallows Hirundo rustica signal body condition during winter moult

The determinants and function of pigmentation of feathers and other tissues have been the focus of a large number of studies, particularly with respect to socio‐sexual communication. However, many birds exhibit depigmented white spots or bars on their feathers whose function is poorly understood. Here we assess whether white feather spots reflect phenotypic condition at the time of moult by investigating the covariation between spot size or shape and condition‐dependent feather growth rate, as gauged by width of the growth bars on the tail feathers of Barn Swallows. We found that feathers with higher growth rates had larger, less rounded white spots. In addition, variance in spot perimeter for a given spot area was larger in males than in females. This study is the first to provide evidence that features of white markings on feathers directly reflect body condition at the time of moult and can therefore reliably signal phenotypic quality in the context of socio‐sexual communication. In addition, the study highlights the potential communication function of the shape and not just the size of colour signals.     

Feather growth bands and photoperiod

Growth bands are alternate dark/light bands perpendicular to the feather rachis. Previous studies indicate that pairs of dark/light bands are grown every 24h, with light bands being produced at night, and dark ones during the day. Thus, the dark:light width ratio could reflect the photoperiod under which a feather was grown. We tested this hypothesis by inducing feathers to grow under contrasting photoperiods, using red‐legged partridges Alectoris rufa as a model species. We first validated the assumption that a pair of dark/light band is produced every day. Secondly, we show that dark/light width ratios remain close to 1:1, irrespective of the photoperiod under which feathers were grown. Dark:light width ratios of feathers grown in summer (15 light‐hours: 9 darkness‐hours) and winter solstices (9l: 15d) did not show any consistent pattern of variation within individuals. Thus, the dark/light banding patterns are not simply the product of light regimes and are not indicative of photoperiod. This finding, together with reports of “aberrant” growth band patterns (e.g. two growth bands produced over 24 h instead of one) challenges our current knowledge of growth bands. We propose that the normal circadian periodicity of growth bands is primarily driven by circadian rhythms: band formation starts at a point of critically low physiological activity (e.g. during night resting), and thus every 24 h irrespective of photoperiod. Our experiment emphasises that our knowledge of growth bands is weaker than previously appreciated, and that the study of dark/light band patterns on feathers could shed new light on interesting phenomena such as unusual avian biological rhythms and the functioning of internal clocks. Detecting “aberrant” banding patterns could therefore allow identifying bird species with unusual activity patterns or physiological rhythms.     

Prebasic molt initiation and progress in northern fulmars of the High Arctic: do molt and breeding overlap?

We examined feather molt progress of northern fulmars (Fulmarus glacialis) at Cape Vera in the Canadian High Arctic through opportunistic observation of individuals in flight from 2003 to 2006, and examination of bodies and wings of 127 individuals collected at the site, from 2003 to 2005. We found no evidence suggesting that fulmars shed primary feathers during breeding. Prebasic molt was initiated in the head, neck, sides, belly and back approximately 1 week before hatch. We failed to detect a sex effect on molt progress, but molt among breeders was delayed compared to molt in non- or failed breeders. This study constitutes a baseline we feel may be useful to: (1) researchers interested in feather replacement chronology, wherein feathers are used as sources of biological information; and (2) researchers interested in eventual assessment of relationships among large-scale environmental processes and molt progress in this species, especially in light of predicted changes to Arctic regions.     

Unravelling the migration and moult strategies of a long-distance migrant using stable isotopes: Red Knot Calidris canutus movements in the Americas

For long‐distance migrants, such as many of the shorebirds, understanding the demographic implications of behavioural strategies adopted by individuals is key to understanding how environmental change will affect populations. Stable isotopes have been used in the terrestrial environment to infer migratory strategies of birds but rarely in marine or estuarine systems. Here, we show that the stable isotope ratios of carbon and nitrogen in flight feathers can be used to identify at least three discrete wintering areas of the Red Knot Calidris canutus on the eastern seaboard of the Americas, ranging from southeastern USA to Patagonia and Tierra del Fuego. In spring, birds migrate northwards via Delaware Bay, in the northeastern USA, the last stopping point before arrival in Arctic breeding areas, where they fatten up on eggs of spawning Horseshoe Crabs Limulus polyphemus. The isotope ratios of feather samples taken from birds caught in the Bay during May 2003 were compared with feathers obtained from known wintering areas in Florida (USA), Bahia Lomas (Chile) and Rio Grande (Argentina). In May 2003, 30% of birds passing through the Bay had Florida‐type ‘signatures’, 58% were Bahia Lomas‐type, 6% were Rio Grande‐type and 7% were unclassified. Some of the southern wintering birds had started moulting flight feathers in northern areas, suspended this, and then finished their moult in the wintering areas, whereas others flew straight to the wintering areas before commencing moult. This study shows that stable isotopes can be used to infer migratory strategies of coastal‐feeding shorebirds and provides the basis for identifying the moult strategy and wintering areas of birds passing through Delaware Bay. Coupled with banding and marking birds as individuals, stable isotopes provide a powerful tool for estimating population‐specific demographic parameters and, in this case, further our understanding of the migration systems of the declining Nearctic populations of Red Knot.     

Complex social behaviour can select for variability in visual features: a case study in Polistes wasps

The ability to recognize individuals is common in animals; however, we know little about why the phenotypic variability necessary for individual recognition has evolved in some animals but not others. One possibility is that natural selection favours variability in some social contexts but not in others. Polistes fuscatus wasps have variable facial and abdominal markings used for individual recognition within their complex societies. Here, I explore whether social behaviour can select for variability by examining the relationship between social behaviour and variability in visual features (marking variability) across social wasp taxa. Analysis using a concentrated changes test demonstrates that marking variability is significantly associated with nesting strategy. Species with flexible nest-founding strategies have highly variable markings, whereas species without flexible nest-founding strategies have low marking variability. These results suggest that: (i) individual recognition may be widespread in the social wasps, and (ii) natural selection may play a role in the origin and maintenance of the variable distinctive markings. Theoretical and empirical evidence suggests that species with flexible nesting strategies have reproductive transactions, a type of complex social behaviour predicted to require individual recognition. Therefore, the reproductive transactions of flexible species may select for highly variable individuals who are easy to identify as individuals. Further, selection for distinctiveness may provide an alternative explanation for the evolution of phenotypic diversity.     

Feather melanin and microstructure variation in dark‐eyed junco Junco hyemalis across an elevational gradient in the Selkirk Mountains

Variation in feather melanism and microstructure can arise through sexual selection and ecological functional drivers. Melanin‐based plumage traits are associated with sexual dichromatism and the intensity of sexual selection in many avian species, but also have several ecological benefits such as protection against ultra‐violet (UV) radiation, camouflage, and feather strength. Additionally, feather microstructure influences thermoregulation. Plumage variation across species is well documented; however, the relative role of sexual selection and ecological drivers in intra‐specific and within‐population variation is less established. We investigated UV reflectance, melanism, and feather microstructure in a population of Oregon dark‐eyed juncos Junco hyemalis oreganus between high (1900–2200 m a.s.l.) and low (450–800 m a.s.l.) elevations in the Selkirk Mountains to evaluate potential sexual selection and ecological drivers of variation. We found no difference in UV reflectance or lightness (melanism) of head feathers between elevations, but individuals at high elevation had lighter (less melanism) and less brown (less pheomelanin) body contour feathers than at low elevations. High elevation individuals also had longer contour feathers with more pronounced plumulaceous regions. Sexual dichromatism did not vary between elevations, leading us to reject sexual selection in favour of ecological functional drivers of plumage variation in this system. To our knowledge, this is the first study to identify within‐population differences in feather melanism and microstructure between different elevations.     

Population differences in the structure and coloration of great tit contour feathers

Contour feathers cover most of the avian body and play critical roles in insulation, social communication, aerodynamics, and water repellency. Feather production is costly and the development of the optimum characteristics for each function may be constrained by limited resources or time, and possibly also lead to trade‐offs among the different characteristics. Populations exposed to different environmental conditions may face different selective pressures, resulting in differences in feather structure and coloration, particularly in species with large geographical distributions. Three resident populations of great tit Parus major L. from different latitudes differed in feather structure and coloration. Individuals from the central population exhibited less dense and longer contour feathers, with a higher proportion of plumulaceous barbs than either northern or southern birds, which did not differ in their feather structure. Ultraviolet reflectance and brightness of the yellow of the contour feathers of the breast was higher for the southern than for the northern population. Birds with greener plumage (higher hue) had less dense but longer feathers, independently of the population of origin. Differences in feather structure across populations appear to be unrelated to the contour feather colour characteristics except for hue. Nutritional and time constraints during molt might explain the pattern of feather structure, whereas varying sexual selection pressure might underlie the coloration patterns observed. Our results suggest that different selective pressures or constraints shape contour feather traits in populations exposed to varying environmental conditions. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 82–91.     

Red-winged blackbirds Agelaius phoeniceus use carotenoid and melanin pigments to color their epaulets

Over the past three decades, the red‐winged blackbird Agelaius phoeniceus has served as a model species for studies of sexual selection and the evolution of ornamental traits. Particular attention has been paid to the role of the colorful red‐and‐yellow epaulets that are striking in males but reduced in females and juveniles. It has been assumed that carotenoid pigments bestow the brilliant red and yellow colors on epaulet feathers, but this has never been tested biochemically. Here, we use high‐performance liquid chromatography (HPLC) to describe the pigments present in these colorful feathers. Two red ketocarotenoids (astaxanthin and canthaxanthin) are responsible for the bright red hue of epaulets. Two yellow dietary precursors pigments (lutein and zeaxanthin) are also present in moderately high concentrations in red feathers. After extracting carotenoids, however, red feathers remained deep brown in color. HPLC tests show that melanin pigments (primarily eumelanin) are also found in the red‐pigmented barbules of epaulet feathers, at an approximately equal concentration to carotenoids. This appears to be an uncommon feature of carotenoid‐based ornamental plumage in birds, as was shown by comparable analyses of melanin in the yellow feathers of male American goldfinches Carduelis tristis and the red feathers of northern cardinals Cardinalis cardinalis, in which we detected virtually no melanins. Furthermore, the yellow bordering feathers of male epaulets are devoid of carotenoids (except when tinged with a carotenoid‐derived pink coloration on occasion) and instead are comprised of a high concentration of primarily phaeomelanin pigments. The dual pigment composition of red epaulet feathers and the melanin‐only basis for yellow coloration may have important implications for the honesty‐reinforcing mechanisms underlying ornamental epaulets in red‐winged blackbirds, and shed light on the difficulties researchers have had to date in characterizing the signaling function of this trait. As in several other birds, the melanic nature of feathers may explain why epaulets are used largely to settle aggressive contests rather than to attract mates.     

Molted feathers from clay licks in Peru provide DNA for three large macaws (Ara ararauna, A. chloropterus, and A. macao)

ABSTRACT Conservation genetic analyses of wildlife have increased greatly in the past 10 yr, yet genetic studies of parrots are rare because of difficulties associated with capturing them and obtaining samples. Recent studies have demonstrated that molted feathers can provide a useful source of DNA, but success rates have varied considerably among studies. Our objective was to determine if molted macaw feathers from Blue‐and‐yellow Macaws (Ara ararauna), Scarlet Macaws (A. macao), and Red‐and‐green Macaws (A. chloropterus) collected from rainforest geophagy sites called clay licks could provide a good source of DNA for population genetic studies. Specific objectives were to determine (1) how nuclear DNA microsatellite amplification success and genotyping error rates for plucked macaw feathers compared to those for molted feathers collected from clay licks in the Amazon rainforest, and (2) if feather size, feather condition, species, or extraction method affected microsatellite amplification success or genotyping error rates from molted feathers. Amplification success and error rates were calculated using duplicate analyses of four microsatellite loci. We found that plucked feathers were an excellent source of DNA, with significantly higher success rates (P < 0.0001) and lower error rates (P= 0.0002) than for molted feathers. However, relatively high success rates (75.6%) were obtained for molted feathers, with a genotyping error rate of 11.7%. For molted feathers, we had higher success rates and lower error rates for large feathers than small feathers and for feathers in good condition than feathers that were moldy and broken when collected. We also found that longer incubation times and lower elution volumes yielded the highest quality DNA when extracting with the Qiagen DNeasy tissue kit. Our study demonstrates that molted feathers can be a valuable source of genetic material even in the challenging conditions of tropical rainforests, and our results provide valuable information for maximizing DNA amplification success rates when working with shed feathers of parrots.     

Balancing selection maintains cryptic colour morphs

Animals display incredibly diverse colour patterns, a testament to evolution's endless innovation in shaping life. In many species, the interplay between males and females in the pursuit of mates has driven the evolution of a myriad of colour forms, from the flashy peacock tail feathers to the tiniest colour markings in damselflies. In others, colour provides crypsis by allowing to blend into the background and to escape the eyes of predators. While the obvious benefits of this dazzling diversity for reproduction and survival seem straightforward, its maintenance is not. Theory predicts that genetic drift and various forms of selection reduce variation over time, making the persistence of colour variants over generations a puzzle. In this issue of Molecular Ecology, Lindtke et al. ( 2017 ) study the cryptic colour morphs of Timema cristinae walking sticks to shed light on the genetic architecture and mechanisms that allow colour polymorphism maintenance over long timescales. By combining genome‐wide data with phenotyping information from natural populations, they were able to map the green and melanistic colour to one genomic region with highly reduced effective recombination rate between two main chromosomal variants, consistent with an inversion polymorphism. These two main chromosomal variants showed geographically widespread heterozygote excess, and genomic signatures consistent with long‐term balancing selection. A younger chromosomal variant was detected for the third morph, the green‐striped colour morphs, in the same genomic regions as the melanistic and the green‐unstriped morphs. Together, these results suggest that the genetic architecture of cryptic T. cristinae morphs is caused by nonrecombining genomic blocks that have been maintained over extended time periods by balancing selection making this study one of the few available empirical examples documenting that balancing selection of various forms may play an important role in maintaining adaptive genetic variation in nature.     

Population genetic connectivity of an endemic New Zealand passerine after large‐scale local extirpations: a model of re‐colonization potential

Little is known about how a 70% loss of native forests has affected the genetic connectivity of remnant bird populations in New Zealand. We use the common and widely distributed New Zealand Bellbird Anthornis melanura as an indicator species of population connectivity for well‐flighted birds. Using eight microsatellite loci, we identified five main genetic populations in the North Island, South Island, sub‐Antarctic Auckland Islands and two small remnant island populations adjacent to a large region of avian extirpations in northern North Island. Only one remnant island population, on a 30‐year‐old conservation reserve at Tiritiri Matangi, displayed a clear signature of recent genetic bottleneck. The 7% migration rate at Tiritiri Matangi indicates that bottlenecks can be maintained despite habitat rehabilitation, possibly through behavioural barriers to gene flow. Adjacent to the same extirpation zone, Bellbirds on the Poor Knights Islands were found to have low genetic diversity and low re‐colonization potential. Two gaps concordant with deforestation patterns separated the Kapiti Coast of southern North Island from populations to both the north and the south. In summary, we identified linked avian habitats, as well as isolated and inbred populations and suggest that Bellbirds are good re‐colonizers. We emphasize the importance of genetic studies that assess animal dispersal among newly rehabilitated habitat patches.     

Development of diagnostic microsatellite markers from whole‐genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone

Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole‐genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high‐resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species.     

Morphological and plumage colour variation in the Réunion grey white‐eye (Aves: Zosterops borbonicus): assessing the role of selection

The Réunion grey white‐eye (Zosterops borbonicus), a small passerine endemic to the island of Réunion (Mascarene archipelago), constitutes an extraordinary case of phenotypic variation within a bird species, with conspicuous plumage colour differentiation at a microgeographical scale. To understand whether natural selection could explain such variability, we compared patterns of variation in morphological and plumage colour traits within and among populations. To quantify morphological variation, we used measurements obtained by Frank Gill in the 1960s from 239 individuals collected in 60 localities distributed over the entire island of Réunion. To quantify colour variation, we measured the reflectance spectra of plumage patches of 50 males from a subset of Gill's specimens belonging to the five recognized plumage colour variants and used a visual model to project these colours in an avian‐appropriate, tetrachromatic, colour space. We found that variants occupy different regions of the avian colour space and that between‐variant differences for most plumage patches could be discriminated by the birds. Differences in morphology were also detected, but these were, in general, smaller than colour differences. Overall, we found that variation in both plumage colour and morphology among variants is greater than would be expected if genetic drift alone was responsible for phenotypic divergence. As the plumage colour variants correspond to four geographical forms, our results suggest that phenotypic evolution in the Réunion grey white‐eye is at least partly explained by divergent selection in different habitats or regions. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 459–473.     

Isolation‐driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae)

Lineage, or true ‘species’, trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene‐tree heterogeneity. Problems with inferring species trees because of excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single‐locus studies, forcing the revision of biogeographic scenarios driving divergence. Here, we use 21 nuclear loci from regional populations to re‐evaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at approximately 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between data sets within the major lineages. Coalescent‐based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns.     

Manta Matcher: automated photographic identification of manta rays using keypoint features

For species which bear unique markings, such as natural spot patterning, field work has become increasingly more reliant on visual identification to recognize and catalog particular specimens or to monitor individuals within populations. While many species of interest exhibit characteristic markings that in principle allow individuals to be identified from photographs, scientists are often faced with the task of matching observations against databases of hundreds or thousands of images. We present a novel technique for automated identification of manta rays (Manta alfredi and Manta birostris) by means of a pattern‐matching algorithm applied to images of their ventral surface area. Automated visual identification has recently been developed for several species. However, such methods are typically limited to animals that can be photographed above water, or whose markings exhibit high contrast and appear in regular constellations. While manta rays bear natural patterning across their ventral surface, these patterns vary greatly in their size, shape, contrast, and spatial distribution. Our method is the first to have proven successful at achieving high matching accuracies on a large corpus of manta ray images taken under challenging underwater conditions. Our method is based on automated extraction and matching of keypoint features using the Scale‐Invariant Feature Transform (SIFT) algorithm. In order to cope with the considerable variation in quality of underwater photographs, we also incorporate preprocessing and image enhancement steps. Furthermore, we use a novel pattern‐matching approach that results in better accuracy than the standard SIFT approach and other alternative methods. We present quantitative evaluation results on a data set of 720 images of manta rays taken under widely different conditions. We describe a novel automated pattern representation and matching method that can be used to identify individual manta rays from photographs. The method has been incorporated into a website (mantamatcher.org) which will serve as a global resource for ecological and conservation research. It will allow researchers to manage and track sightings data to establish important life‐history parameters as well as determine other ecological data such as abundance, range, movement patterns, and structure of manta ray populations across the world.