Birds of a feather: Comprehensive plumage colour analysis for a revised subspecies classification of the Chestnut-winged Babbler (Cyanoderma erythropterum) species complex

BackgroundThe taxonomy of the Collared Owlet (Glaucidium brodiei) species complex is confused owing to great individual variation in plumage colouration seemingly unrelated to their distribution. Although generally recognised as a single species, vocal differences among the subspecies have been noted by field recordists. However, there is no study assessing the vocal differences among these four subspecies.MethodsWe obtained 76 sound recordings of the G. brodiei species complex comprising all four subspecies. We conducted bioacoustic examinations using principal component analysis and the Isler criterion to quantitatively test species boundaries within the G. brodiei complex. In addition, we compared plumage colouration among 13 specimens of the G. brodiei complex deposited at the Natural History Museum at Tring, UK and the Lee Kong Chian Natural History Museum, Singapore to ascertain the presence of plumage differences across taxa.ResultsWe found the Bornean and Sumatran populations vocally similar to each other, but distinctly different from the mainland and Taiwan populations. The vocal pattern seems to corroborate plumage distinctions in the colouration of neck collars: the Bornean and Sumatran taxa share a white neck collar, whereas the continental and Taiwan taxa share a rufous neck collar.ConclusionsWe propose the taxonomic elevation of the Sumatran and Bornean populations to species level as Sunda Owlet G. sylvaticum, with one subspecies on Sumatra (G. s. sylvaticum) and Borneo (G. s. borneense) each. Our study corroborates the importance of bioacoustics in ascertaining species boundaries in non-passerines, and emphasises the significance of incorporating multiple species delimitation approaches when making taxonomic decisions.

Beyond a morphological paradox: Complicated phylogenetic relationships of the parrotbills (Paradoxornithidae, Aves)

The biodiversity of the Neotropics is considerable, but it is likely underestimated owing to gaps in sampling effort and a focus on using morphological features of animals to determine species differences rather than divergence in their mating signals and behavior. Recent multi-trait analyses incorporating morphological, plumage, and vocal data have allowed for more accurate quantification of tropical biodiversity. We present a comprehensive study of morphological features, plumage, and vocalizations of the Neotropical resident Rufous-capped Warbler (Basileuterus rufifrons). This species’ taxonomic status is controversial because the B. r. salvini subspecies is intermediate in plumage coloration between the neighboring B. r. delattrii and B. r. rufifrons subspecies. Using morphological and spectral plumage measurements of field and museum specimens, as well as analyses of vocalizations from field recordings and sound libraries, we compared phenotypes of all 8 currently recognized Rufous-capped Warbler subspecies, with an emphasis on delattrii, rufifrons, and salvini. We found that delattrii and rufifrons differ significantly in morphology and plumage, and that salvini is similar to rufifrons in morphology and some plumage features. Vocalizations fall into 2 distinct groups, delattrii and rufifrons-salvini, which differ in multiple spectro-temporal characteristics with no overlap between them, even among individuals in the delattrii–rufifrons zone of sympatry. Our results therefore suggest that Rufous-capped Warblers comprise 2 distinct groups: Rufous-capped Warblers (B. r. rufifrons and salvini as well as B. r. caudatus, dugesi, and jouyi) and Chestnut-capped Warblers (B. r. delattrii as well as B. r. actuosus and mesochrysus). Future genomic analysis of samples from multiple sites in Mexico and Central America will further refine our assessment of range-wide phenotypic and genetic divergence in this species complex.

he Arctic warbler (Phylloscopus borealis) species complex is commonly present in the Palearctic region. By 2014, the three bird subspecies were split into three species, Arctic warbler (P. borealis), Japanese leaf warbler (P. xanthodryas), and Kamchatka leaf warbler (P. examinandus), based on different breeding areas and distinct vocalizations. However, their similar coloration and body size make it difficult to distinguish these species in the nonbreeding season. Taiwan is located in the potential migration routes of the Arctic warbler species complex; however, no confirmed record of P. xanthodryas and P. examinandus exists. In this study, we compared the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences of samples from breeding sites during the breeding season and confirmed that the three species could be distinguished based on CO1 gene sequences. We also examined the species of the Arctic warbler species complex samples collected from eastern Taiwan. For the first time, we confirmed that all three species visited Taiwan during migration season. In the Taiwanese samples, no clear distinction could be made between species based on plumage coloration and size, indicating that these traits are not reliable for species identification. Reassessment of the CO1 gene sequences of the three species deposited in the Barcode of Life Data System revealed that the taxonomic status needs to be updated for 31.8% of the samples.

Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers.

Intraspecific differences in retinal physiology have been demonstrated in several vertebrate taxa and are often subject to adaptive evolution. Nonetheless, such differences are currently unknown in birds, despite variations in habitat, behaviour and visual stimuli that might influence spectral sensitivity. The parrot Platycercus elegans is a species complex with extreme plumage colour differences between (and sometimes within) subspecies, making it an ideal candidate for intraspecific differences in spectral sensitivity. Here, the visual pigments of P. elegans were fully characterised through molecular sequencing of five visual opsin genes and measurement of their absorbance spectra using microspectrophotometry. Three of the genes, LWS, SW1 and SWS2, encode for proteins similar to those found in other birds; however, both the RH1 and RH2 pigments had polypeptides with carboxyl termini of different lengths and unusual properties that are unknown previously for any vertebrate visual pigment. Specifically, multiple RH2 transcripts and protein variants (short, medium and long) were identified for the first time that are generated by alternative splicing of downstream coding and non-coding exons. Our work provides the first complete characterisation of the visual pigments of a parrot, perhaps the most colourful order of birds, and moreover suggests more variability in avian eyes than hitherto considered.

Speciation phenomena have received considerable attention from geneticists, taxonomists, and evolutionary theorists. A primary impasse to our knowledge has been the paucity of field studies employing direct observations of species in some critical stage of this process. The birds chosen for this study, Blue-winged Warblers (Vermivora pinus) and Golden-winged Warblers (V. chrysoptera), are at a critical point; the parental phenotypes continue to occur although fertile hybrids are produced. We deal with the reproductive relationships of the two species and hybrids. Data from field studies and the literature lead to conclusions about pairing mechanisms, the success of hybrids vs. parental types, and possible factors promoting reproductive isolation as well as those increasing interbreeding. This species complex is ideal for investigations of speciation for several reasons: (1) the zone of sympatry and hybridization is extensive, (2) their history of contact is reasonably well-documented, (3) there are many accounts in the literature of mixed pairs in different areas of sympatry, and (4) field observations are not difficult early in the season since the birds are conspicuous and have rather small territories. The Blue-wing, formerly the more southern species, has expanded its range northward in the last hundred years and is now extensively sympatric with the Golden-wing (Short, 1963; Berger, 1958). When birds intermediate in plumage were discovered in the late 1800's, there was much speculation concerning their origin. Finally Faxon (1913) carefully followed a mixed pair and found that progeny resembling the Brewster's Warbler, one of the intermediate types, resulted from this mating. Unfortunately, the great interest in these species then waned, since the origin of intermediate specimens was no longer a mystery. Only recently have ornithologists begun detailed investigations. Parkes (1951) proposed an interpretation of the inheritance of plumage color and pattern supported by observations of the progeny of mixed pairings. Berger (1958) outlined historical changes and the ecological status of the two species and hybrids in the Great Lakes states. More recently, Short (1962, 1963), studying the two species and hybrids in several areas of sympatry by detailed analyses of specimens, showed that introgression has taken place. The present study is based mainly on investigations in two areas, but is far from definitive because the situation is complex and ever-changing throughout the area of sympatry. There is great need for more intensive studies in many different areas and over a long period of time; only then will all of the complex processes become clear. This paper is one of a series on song, courtship, ecology and territory in Blue-winged Warblers, Golden-winged Warblers and their hybrids (Ficken and Ficken, 1966 in press a, b, c.)

Studies of the patterns of diversification of birds on islands have contributed a great deal to the development of evolutionary theory. In white-winged fairy-wrens, Malurus leucopterus, mainland males develop a striking blue nuptial plumage whereas those on nearby islands develop black nuptial plumage. We explore the proximate basis for this divergence by combining microstructural feather analysis with an investigation of genetic variation at the melanocortin-1 receptor locus (MC1R). Fourier analysis revealed that the medullary keratin matrix (spongy layer) of the feather barbs of blue males was ordered at the appropriate nanoscale to produce the observed blue colour by coherent light scattering. Surprisingly, the feather barbs of black males also contained a spongy layer that could produce a similar blue colour. However, black males had more melanin in their barbs than blue males, and this melanin may effectively mask any structural colour produced by the spongy layer. Moreover, the presence of this spongy layer suggests that black island males evolved from a blue-plumaged ancestor. We also document concordant patterns of variation at the MC1R locus, as five amino acid substitutions were perfectly associated with the divergent blue and black plumage phenotypes. Thus, with the possible involvement of a melanocortin receptor locus, increased melanin density may mask the blue-producing microstructure in black island males, resulting in the divergence of plumage coloration between mainland and island white-winged fairy-wrens. Such mechanisms may also be responsible for plumage colour diversity across broader geographical and evolutionary scales.

Signaling stress? An analysis of phaeomelanin-based plumage color and individual corticosterone levels at two temporal scales in North American barn swallows, Hirundo rustica erythrogaster

AimPheomelanin is a pigment responsible for yellowish‐to‐reddish colours of vertebrate teguments. Its biosynthesis is favoured under high concentration of intracellular thiols, which, in turn, can depend on the environmental exposure to sulphur. Thus, pheomelanin production should be more intense and frequent in environments characterized by high level of sulphur, such as volcanic regions. In this study, we aimed at addressing this hypothesis by investigating variation in plumage colour of insular populations of the cosmopolitan barn owl (Tyto alba species complex) according to the presence of soils of volcanic origin (i.e. andosols) and recent volcanic activity.LocationWorld.TaxonBarn owl species complex.MethodsWe measured plumage colouration of more than 2000 museum specimens from 50 islands and archipelagos worldwide. We then compared plumage colouration between populations living on volcanic (i.e. where andosols and/or recent volcanic activity are present) and non‐volcanic islands/archipelagos.ResultsConsistently with the prediction, plumage colouration is significantly darker (i.e. pheomelanic) on islands/archipelagos where andosols and/or recent volcanic activity are present than absent, although this environmental factor explains a small fraction of plumage colour variability across islands (<10%). Similar results were obtained when specimens' sex and climatic predictors were included in the analyses.Main ConclusionsBecause excessive intracellular levels of thiols can be toxic, pheomelanin synthesis may function as a mechanism keeping these compounds below the toxicity threshold and limiting their detrimental effects on physiology. Darker plumage may also be favoured because it promotes background matching against the dark environment typical of volcanic islands (dense vegetation cover and/or dark soil). Our results add to the little evidence that the environmental exposure of compounds that are involved in melanin biosynthesis can affect animal pigmentation and suggest that soil composition may be a factor that affects melanogenesis, possibly contributing to generate spatial variation in pheomelanin‐based traits in animals.

AimClimatic gradients shape geographic variation in phenotypic traits that are involved in animal thermoregulation. Therefore, increasing temperatures under global warming are expected to cause change over time in traits that show predictable spatial patterns according to environmental clines (body and appendage size, tegument coloration), as well exemplified by biogeographic rules and shown by increasing literature at a local scale. However, whether temporal shifts in phenotypic traits vary spatially according to the magnitude of the change in local climatic conditions is still unknown.LocationWorld.TaxonBarn owl species complex (Tyto alba group).MethodsBy using thousands of museum specimens collected across the globe from 1901 to 2018, we calculated within‐population change over time in wing length, bill length and melanin‐based plumage coloration and examined whether these trends differed across geographic regions, latitudes and gradients of climate changes.ResultsWe showed that populations exposed to an increasing warmer climate were subjected to a more marked decrease in body size, as gauged by wing length, and also absolute bill length that displayed a similar, although less steep, pattern of shrinking over time. In addition, phaeomelanin‐based ventral plumage colour has become paler in regions where the climate changed into warmer and drier, and darker where both temperature and precipitation increased.Main ConclusionsThese trends are generally coherent with the predictions based on Bergmann's and Gloger's rules, but not Allen's rule, and suggest that temporal shifts in body size and tegument colour depend on the magnitude of the alteration in climatic conditions, with populations living in regions where the climate has changed the most that are subjected to more marked phenotypic changes. Spatio‐temporal variation in climate has driven within‐species phenotypic clines, and it is expected to increase differences among populations according to the predicted further climate change.

We present a phylogenetic analysis of relationships among members of the Amazona ochrocephala species complex of parrots, a broadly distributed group in Middle and South America that has been a “taxonomic headache.” Mitochondrial DNA sequence data are used to infer phylogenetic relationships among most of the named subspecies in the complex. Sequence-based phylogenies show that Middle American subspecies included in the analysis are reciprocally monophyletic, but subspecies described for South America do not reflect patterns of genetic variation. Samples from the lower Amazon cluster with samples collected in western Amazonia—not with samples from Colombia and Venezuela, as was predicted by subspecies classification. All subspecies of the complex are more closely related to one another than to other Amazona species, and division of the complex into three species (A. ochrocephala, A. auropalliata, and A. oratrix) is not supported by our data. Divergence-date estimates suggest that these parrots arrived in Middle America after the Panama land-bridge formed, and then expanded and diversified rapidly. As in Middle America, diversification of the group in South America occurred during the Pleistocene, possibly driven by changes in distribution of forest habitat.

Cucullanus pinnai has been divided in two subspecies (C. pinnai pinnai and C. pinnai pterodorasi) based on the morphology of oesophastome. While C. pinnai pinnai apparently shows low host specificity and broad geographic occurrence, with certain morphological variations, C. pinnai pterodorasi was reported once, parasitizing Pterodoras granulosus. We used an integrative taxonomic approach to evaluate whether or not populations of C. pinnai pinnai from Trychomycterus spegazzinii (Escoipe River, Argentina) and Pimelodus fur (Miranda River, Brazil), and of C. pinnai pterodorasi from Pterodoras granulosus (Miranda River, Brazil) are conspecific. Parasites were observed using light microscopy and genetically characterized based on partial sequences of the 18S and 28S rDNA, ITS1-5.8S-ITS2, and COI mtDNA. Phylogenies were reconstructed and the Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (bPTP), and Automatic Barcode Gap Discovery (ABGD) were used for species delimitation purposes. The present samples formed well-supported monophyletic assemblages, corroborating in part the results of morphological analyses; however, they grouped according to geographic origin. Species delimitation suggested conspecificity of C. pinnai pinnai with C. pinnai pterodorasi from Brazil; consequently, the morphology of oesophastome may be an intraspecific variation. Results also indicated that C. pinnai may represent a species complex as samples from Argentina were suggestive of an independent specific entity. However, definitive affirmations are premature, since there is no autapomorphy for separating C. pinnai from Brazil and Argentina and sampling was limited to three host species from two river basins. The phylogenetic reconstructions also confirmed the artificiality of some genera within Cucullanidae.

We present a phylogenetic analysis of relationships among members of the Amazona ochrocephala species complex of parrots, a broadly distributed group in Middle and South America that has been a “taxonomic headache.” Mitochondrial DNA sequence data are used to infer phylogenetic relationships among most of the named subspecies in the complex. Sequence-based phylogenies show that Middle American subspecies included in the analysis are reciprocally monophyletic, but subspecies described for South America do not reflect patterns of genetic variation. Samples from the lower Amazon cluster with samples collected in western Amazonia—not with samples from Colombia and Venezuela, as was predicted by subspecies classification. All subspecies of the complex are more closely related to one another than to other Amazona species, and division of the complex into three species (A. ochrocephala, A. auropalliata, and A. oratrix) is not supported by our data. Divergence-date estimates suggest that these parrots ar...