Plumage Variation Research Articles

Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird.

The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue-throated populations (Sierra Madre del Sur); two groups of amethyst-throated populations (Trans-Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39-0.57million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue- and amethyst-throated populations does not correspond to the 2-MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species' suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest-interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.

Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of white wagtail Motacilla alba (Aves: Passeriformes)

We studied the phylogeography and population history of the white wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of white wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in central and south Europe; and clade SE was distributed in central and east Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of east Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.

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

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

Novel insights into the historical biogeography of the streak-breasted scimitar babbler complex (Aves: Timaliidae: Pomatorhinus ruficollis complex)

Abstract The Streak-breasted Scimitar Babblers of the Pomatorhinus ruficollis species complex are found in most of the forested habitats across southern and eastern Asia. The diversification history of this group is obscured by high plumage variation across populations and conflicting genetic signal across loci. We combined genetic and geographic data from several recent studies to investigate how these species diversified across China using both phylogenetic and ecological niche modeling analyses. These two lines of evidence are consistent in showing that two well-sampled species, P. reconditus and P. nigrostellatus, in central and southern China respectively, likely experienced a history of isolation and expansion as suitable habitat contracted during the last interglacial and expanded in patchy extent during the glacial maximum. The genetic analysis showed that populations of P. nigrostellatus on Hainan Island are very similar to the ones in nearby mainland southern China. We recovered two well-supported clades within P. reconditus that were not geographically structured with both containing individuals from the same localities across central China. This phylogenetic result corresponded to the ecological niche models that showed expansion from refugia since the last interglacial. This study illustrates the value of using an integrative approach and detailed geographic sampling to help understand the recent diversification of birds in China.

Genetic divergence of Troglodytes troglodytes islandicus from other subspecies of Eurasian wren in northwestern Europe

The Icelandic subspecies of Eurasian wren Troglodytes troglodytes islandicus has been described as a large wren which is sedentary on the island. It is one member of a large passerine complex which is widely distributed over the Holarctic except the Arctic. The taxonomic affiliation of the subspecies is mainly based on variation in plumage and on the song complexity. This study investigated the genetic differentiation of T. t. islandicus among the Eurasian wren subspecies in northwestern Europe, and especially in relation to its geographically proximate populations in the Faroe Islands, Scotland, southern Norway, Sweden and Denmark. Troglodytes t. islandicus and the Faroese subspecies (T. t. borealis) were genetically differentiated from the other subspecies (T. t. indigenus and T. t. troglodytes) with an estimated time of divergence from this group during the last glacial maximum; 21 thousand years before present (KYBP) [44–8]. A clear but a more recent split was observed between T. t. islandicus and T. t. borealis 12 KYBP [28–4].

A taxonomic review of Aramidescajaneus (Aves, Gruiformes, Rallidae) with notes on morphological variation in other species of the genus.

The taxonomy of the polytypic and wide-ranging Gray-necked Wood-rail, Aramides cajaneus is reviewed, based on external morphology and voice. Throughout its distribution, there is extensive plumage variation, much of it taxonomically uninformative. However, through three informative plumage characters, as well as morphometric and vocal variation, three phylogenetic species were identified within what is today known as Aramides cajaneus, all of which already had available names: Aramides albiventris Lawrence, 1868, from southern Mexico to northeastern Costa Rica, Aramides cajaneus (Statius Müller, 1776) (sensu stricto), from southwestern Costa Rica to Argentina, and Aramides avicenniae Stotz, 1992, from a small section of the coast of southeastern Brazil. Aramides albiventris presents extensive plumage variation, but with no geographic structure. The song of Aramides cajaneus and Aramides avicenniae is strikingly and completely different from the song of Aramides albiventris. A previously unnoticed parapatric pattern of distribution of Aramides cajaneus and its congener Aramides saracura in southeastern Brazil is described, and we clarify that the name Aramides plumbeicollis, included in the synonymy of Aramides albiventris, was first made available in 1892, rather than in 1888 as is widely referred. In addition, plumage variation in Aramides ypecaha, Aramides wolfi, and Aramides mangle is discussed.

Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird.

Understanding the patterns and processes that contribute to phenotypic diversity and speciation is a central goal of evolutionary biology. Recently, high-throughput sequencing has provided unprecedented phylogenetic resolution in many lineages that have experienced rapid diversification. The Holarctic redpoll finches (Genus: Acanthis) provide an intriguing example of a recent, phenotypically diverse lineage; traditional sequencing and genotyping methods have failed to detect any genetic differences between currently recognized species, despite marked variation in plumage and morphology within the genus. We examined variation among 20 712 anonymous single nucleotide polymorphisms (SNPs) distributed throughout the redpoll genome in combination with 215 825 SNPs within the redpoll transcriptome, gene expression data and ecological niche modelling to evaluate genetic and ecological differentiation among currently recognized species. Expanding upon previous findings, we present evidence of (i) largely undifferentiated genomes among currently recognized species; (ii) substantial niche overlap across the North American Acanthis range; and (iii) a strong relationship between polygenic patterns of gene expression and continuous phenotypic variation within a sample of redpolls from North America. The patterns we report may be caused by high levels of ongoing gene flow between polymorphic populations, incomplete lineage sorting accompanying very recent or ongoing divergence, variation in cis-regulatory elements, or phenotypic plasticity, but do not support a scenario of prolonged isolation and subsequent secondary contact. Together, these findings highlight ongoing theoretical and computational challenges presented by recent, rapid bouts of phenotypic diversification and provide new insight into the evolutionary dynamics of an intriguing, understudied non-model system.

Cory’s Bittern, <em>Ixobrychus</em> “<em>neoxenus</em>” <em>exilis</em>: morph, mutant, or mixed bag?

Cory’s Bittern (Ixobrychus “neoxenus” exilis) is an enigmatic form, usually referred to as a rare dark colour phase or morph of Least Bittern (Ixobrychus exilis [Gmelin, 1789]). A review of the literature indicates that birds identified as Cory’s Bittern show considerable plumage variation and commonly exhibit multiple plumage anomalies. Temporal and spatial clumping of records shows that they are of irregular occurrence; thus, they do not meet the criteria for recognition as a colour morph. Cory’s Bittern should thus be viewed as a colloquial name that refers to any one of a number of abnormally dark-plumaged, genetically undefined and phenotypically heterogeneous Least Bitterns.

Fecundity selection does not vary along a large geographical cline of trait means in a passerine bird

Local environmental and ecological conditions are commonly expected to result in local adaptation, although there are few examples of variation in phenotypic selection across continent-wide spatial scales. We collected standardized data on selection with respect to the highly variable plumage coloration of pied flycatcher (Ficedula hypoleucaPall.) males from 17 populations across the species' breeding range. The observed selection on multiple male coloration traits via the annual number of fledged young was generally relatively weak. The main aim of the present study, however, was to examine whether the current directional selection estimates are associated with distance to the sympatric area with the collared flycatcher (Ficedula albicollisTemminck), a sister species with which the pied flycatcher is showing character displacement. This pattern was expected because plumage traits in male pied flycatchers are changing with the distance to these areas of sympatry. However, we did not find such a pattern in current selection on coloration. There were no associations between current directional selection on ornamentation and latitude or longitude either. Interestingly, current selection on coloration traits was not associated with the observed mean plumage traits of the populations. Thus, there do not appear to be geographical gradients in current directional fecundity selection on male plumage ornamentation. The results of the present study do not support the idea that constant patterns in directional fecundity selection would play a major role in the maintenance of coloration among populations in this species. By contrast, the tendency for relatively weak mosaic-like variation in selection among populations could reflect just a snapshot of temporally variable, potentially environment-dependent, selection, as suggested by other studies in this system. Such fine-grained variable selection coupled with gene flow could maintain extensive phenotypic variation across populations.(c) 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114, 808-827.

Phenotypic Characterization and Farm Management of Indigenous Chicken Reared in Highland Region of Northern Thailand

The aims of this study were to phenotypically characterize and to describe the production system of Thai indigenous chicken reared by hill tribe people living in the highland region of Phayao province, Northern Thailand. A survey using the random sampling method was carried out in 3 villages consisting of 2 different tribes, Hmong and Mien. Data were recorded of 320 chickens; 160 male and 160 female. Effects of supplemented indigenous microorganism on growth performance of crossbred Thai indigenous chickens were performed using 200 birds. The results showed that Thai indigenous chicken in highland region forms a very heterogeneous character; they exhibited wide variation in color, plumage, comb type, skin color, eye color, shank color, and beak color. The predominant plumage color of Thai native chicken in the region was black followed by red brownish, white and multicolor. The overall means indicated that about 73.5, 55.6, 65.8 and 61.4% of the chickens had pea comb types, black shank color, eye color, and black beak color, respectively. The mean of flock size was less than 10 chickens per household (63.3%). The production systems in the study region were classified into three system; free-ranges, semi free-ranges and semi-intensive. Only 13.3% of the farmers knew about proper vaccination programs, while 88.7% never vaccinated their chicken. Thai indigenous crossbreed chickens that were fed diets containing indigenous microorganisms had a significantly (P<0.05) higher body weight at week 1 and 6 compared to commercial probiotics. The major use of chicken by both Hmong and Mien people is not only for food but also for socio-cultural values. The study also identified that women were more involved in chicken management activities than men. Further research is needed, especially on breeding plans and management practices.

Untangling taxonomic confusion and diversification patterns of the Streak-breasted Scimitar Babblers (Timaliidae: Pomatorhinus ruficollis complex) in southern Asia

Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa – P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a ‘suture’ zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The ‘suture’ zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.

Age and gender related plumage variation of psittacofulvine pigments: the case of the Yellow-faced Parrot Alipiopsitta xanthops

The Yellow-faced Parrot Alipiopsitta xanthops presents considerable phenotypic variation with a belly coloration that may vary from green to yellow-red. Though it has been hypothesized that this variation could be related to sex or age, these possibilities remain untested. We therefore tested these hypotheses by verifying geographical, sexual, and age-related trends in coloration based on museum specimens, wild populations, and captive developing juvenile birds. We found colored belly parrots (CBP) throughout the species distribution of A. xanthops. We found no differences in the proportion of CBP individuals between the two wild populations sampled (overall mean of 8.7%), but the proportion of CBP in museums was higher (32%) indicating that specimens were probably not randomly collected. We also found a skewed sex ratio in museums, as females represented only 25% of the specimens. We found that 37% of museum males had colored bellies, in contrast with only 18% of females; furthermore, colored bellied males presented a greater area of yellow-red patch on their bodies. None of the 16 observed fledglings presented colored bellies. The yellow head coloration slowly grew over the 14 days of observation of 16 nestlings. Together, our results suggest that color variation in the Yellow- faced Parrot seems to be related to both age and gender.

Taxonomy and conservation: a tale of two tinamou species groups (Tinamidae, Crypturellus)

Species delimitation has important consequences for the management of endangered species. Species‐level taxonomy in the genus Crypturellus (Tinamidae) has been based largely on plumage characters and species limits in several groups have been difficult to establish. Because some of the forms of uncertain taxonomic status are currently threatened with extinction, a basic understanding of species limits is crucial not only for taxonomists but also for conservation biologists and managers. We analysed vocal variation to assess species limits in two Crypturellus species‐groups, the red‐legged complex (Crypturellus erythropus and allied forms) and the brown tinamou Crypturellus obsoletus. In the red‐legged complex, where several species‐level taxa have been recognized by some authors, there is no obvious geographic variation in vocalizations and populations appear mostly continuously distributed, with plumage variation largely explicable in terms of environmental conditions. In the brown group, a single species is recognized, but we found marked geographic variation in vocalizations and populations have disjunct distributions; we propose that at least one of the populations in this group likely merits recognition as a separate species. We conclude that incomplete knowledge of patterns of variation in relevant traits in addition to the momentum carried by traditional taxonomy may potentially mislead conservation actions.

Towards Conservation of Omani Local Chicken: Phenotypic Characteristics, Management Practices and Performance Traits

Characterizing local chicken types and their mostly rural production systems is prerequisite for designing and implementing development and conservation programs. This study evaluated the management practices of small-scale chicken keepers and the phenotypic and production traits of their chickens in Oman, where conservation programs for local livestock breeds have currently started. Free-range scavenging was the dominant production system, and logistic regression analysis showed that socio-economic factors such as training in poultry keeping, household income, income from farming and gender of chicken owners influenced feeding, housing, and health care practices (p<0.05). A large variation in plumage and shank colors, comb types and other phenotypic traits within and between Omani chicken populations were observed. Male and female body weight differed (p<0.05), being 1.3±0.65 kg and 1.1±0.86 kg respectively. Flock size averaged 22±7.7 birds per household with 4.8 hens per cock. Clutch size was 12.3±2.85 and annual production 64.5±2.85 eggs per hen. Egg hatchability averaged 88±6.0% and annual chicken mortality across all age and sex categories was 16±1.4%. The strong involvement of women in chicken keeping makes them key stakeholders in future development and conservation programs, but the latter should be preceded by a comprehensive study of the genetic diversity of the Omani chicken populations.

Geographic variation in songs of the Common Yellowthroat

ABSTRACT The Common Yellowthroat (Geothlypis trichas) exhibits widespread geographic variation in plumage, morphology, migratory behavior, and song. In addition, researchers recently found evidence that the Common Yellowthroat has three genetically distinct groups across its North American range: eastern, western, and southwestern. These groups are more genetically similar to other Geothlypis species than to each other, which suggests relatively long-term isolation. I hypothesized that geographic variation in song behavior should reflect these genetic differences. To test this hypothesis, I examined spatial patterns of variation in both note types and acoustic characteristics of song. Consistent with the hypothesis, I found significant differences among the three groups, particularly in frequency measures, internote duration, notes per phrase, and note elaborateness. Within the eastern and western groups, I also found significant song differences among historically recognized subspecies. When comparing we...

Incorporating Color into Integrative Taxonomy: Analysis of the Varied Tit (Sittiparus varius) Complex in East Asia

Species designations are critically important scientific hypotheses that serve as the foundational units in a wide range of biological subdisciplines. A growing realization that some classes of data fail to delimit species under certain conditions has led to increasingly more integrative taxonomies, whereby species discovery and hypothesis testing are based on multiple kinds of data (e.g., morphological, molecular, behavioral, ecological, etc.). However, although most taxonomic descriptions have been based on morphology, some key morphological features, such as color, are rarely quantified and incorporated into integrative taxonomic studies. In this article, we applied a new method of ultraviolet digital photography to measure plumage variation in a color-variable avian species complex, the varied tit (Sittiparus varius). Plumage measurements corroborated species limits defined by morphometric, mitochondrial DNA, and nuclear DNA disjunctions and provided the only evidence for distinguishing two recently evolved species. Importantly, color quantification also provided a justification for lumping putative taxa with no evidence of evolutionary independence. Our revised taxonomy thus refines conservation units for listing and management and clarifies the primary units for evolutionary studies. Species tree analyses, which applied the newly delimited species as operational taxonomic units, revealed a robust phylogenetic hypothesis for the group that establishes a foundation for future biogeographic analyses. This study demonstrates how digital photography can be used to incorporate color character variation into integrative taxonomies, which should lead to more informed, more rigorous, and more accurate assessments of biodiversity. [Color, digital photography, integrative taxonomy, Sittiparus varius, species delimitation, varied tit.].

Current and Historical Extent of Phenotypic Variation in the Tufted and Black-crested Titmouse (Paridae) Hybrid Zone in the Southern Great Plains

Hybrid zones, where phenotypically distinct populations interbreed, should expand or contract until reaching a balance between selection and dispersal. Few studies examine multiple contacts within one species complex to compare how their extent changes over time. Black-crested and Tufted Titmice (Baeolophus atricristatus and B. bicolor) hybridize extensively within a narrow zone in Texas and southwestern Oklahoma. In Texas, hybridization has been occurring for several thousands of years, while evidence suggests the southwestern Oklahoma contact is more recent, beginning within the past century. We quantify plumage and morphology of the two species across both the younger and older hybrid zones and compare the current and historical extent of phenotypic variation in the older Texas contact with that in the younger Oklahoma contact. Variation in plumage between species is similar in the younger and older contacts, while overlap in morphological characters is broader in the older contact. Recently and historically surveyed transects in the older zone have similar cline widths, indicating selection, at least on crest and forehead plumage, has reached equilibrium with dispersal over the time periods involved (comparing both the historically surveyed data from 1955 vs. the recently surveyed data from the 2000s in Texas). In the recently surveyed younger Oklahoma contact, cline width is narrower, indicating potential for expansion if it follows the course of the older contact. This temporal complexity should make this species complex a productive system for future work, using plumage and additional traits such as song and genetics, on the relative influences of both natural and sexual selection on the evolution of reproductive isolation.

Taxonomy, distribution, natural history and conservation of the Russet-mantled Foliage-gleaner Syndactyla dimidiata (Pelzeln, 1859) (Aves: Furnariidae).

Russet-mantled Foliage-gleaner is an extremely poorly known species, the range of which is centered in the Brazilian Cerrado, where it inhabits riparian forests. Two subspecies are recognized, but the limits of their ranges are controversial. Furthermore, it was recently suggested that the species is one of the few in the family Furnariidae to show sexual dichromatism. In this paper we examined the plumage coloration and morphometrics of 33 study skins (85% of the available specimens). We conclude that the geographic variation and sexual dichromatism reported for S. dimidiata originated from misinterpretation of the plumage variation observed in this species, which is best considered monotypic. We also present natural history data on Russet-mantled Foliage-gleaners and suggest considering it a globally Vulnerable species.

British Ornithologists' Union Records Committee: 42nd Report (October 2013)

British Ornithologists' Union Records Committee: 42nd Report (October 2013)

Incubation shifts of northern fulmars Fulmarus glacialis in the Canadian high Arctic determined by digital photography

Determining the incubation pattern of northern fulmars (Fulmarus glacialis) at Canadian Arctic colonies is difficult, in part due to challenges with accessing nests and due, in part, to similarities in colour morphs which can be hard to distinguish. We used digital photographs of incubating birds taken ~daily at 49 breeding sites during the second half of the incubation period and compared inter-observer variation in distinguishing incubation shifts by each member of the pair. Using this method gave similar results when different subsets of sites were included and the assessment of incubation shifts by three different people produced similar results, yielding a mean shift duration of 6.4 days. Provided pairs with suitable variation in plumage or bill colour are selected, our results demonstrate that a remote camera technique can provide precise data to assess fulmar responses to annual environmental conditions for feeding and breeding.