Melanin coloration in New World orioles I: carotenoid masking and pigment dichromatism in the orchard oriole complex

Carotenoids produce the brilliant red, orange, and yellow colors of many animals. However, melanin pigments can also confer some of these same hues. Because carotenoid and melanin colors are produced in different ways and may serve different signaling functions, either within or between species, it is important to establish whether one or both types of pigment are responsible for coloration. We have discovered what appears to be an evolutionary switch from carotenoid- to melanin-based color in two sexually dichromatic New World orioles. Using a combination of reflectance spectrometry and chromatographic analyses of plumage pigments, we found that the chestnut plumage of adult male orchard orioles Icterus spurius is produced predominantly by phaeomelanins. Orchard oriole feathers also contain carotenoids, which appear to be masked by the high concentration of phaeomelanins. In contrast, both carotenoids and phaeomelanins appear to contribute to color in adult male Fuertes's orioles I. fuertesi . Moreover, yellow yearling male and female plumage in both species is produced by carotenoids alone. The masking of carotenoids with phaeomelanins in orchard orioles is interesting in light of the signaling roles that carotenoids are thought to play. In addition, these plumage differences produce a unique case of age and sexual pigment dimorphism in orchard and Fuertes's orioles.     

A molecular phylogeny of the New World orioles (Icterus): the importance of dense taxon sampling.

We sequenced 2005 bp of the mitochondrial ND2 and cytochrome b genes from the 25 recognized species of New World orioles (Icterus). Our data confirmed the monophyly of Icterus and produced a well-resolved phylogeny showing three main clades of orioles. We also sequenced multiple subspecies for most polytypic taxa. Our findings demonstrated the importance of dense taxon sampling below the species level in two ways. First, we found evidence that two species are polyphyletic, I. galbula (Northern oriole) and I. dominicensis (Black-cowled oriole). Choosing different subspecies from either of these taxa would lead to different species-level phylogenies. Second, adding subspecies even to monophyletic groups produced a bootstrap tree with significantly more support. Of the two genes that we used, ND2 provided more resolution than did cytochrome b. ND2 evolved up to 40% faster than cytochrome b, yet shows a higher saturation threshold. Our findings suggest that ND2 may be superior to cytochrome b for resolving species-level phylogenies in passerine birds.     

Mapping uncertainty and phylogenetic uncertainty in ancestral character state reconstruction: an example in the moss genus Brachytheciastrum

The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete morphological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (II) optimized by ML onto each of a Bayesian sample of trees; and (III) sampled by a MCMC visiting the space of a Bayesian sample of trees affects the reconstruction of ancestral states in the moss genus Brachytheciastrum. In the first two methods, the choice of a single- or two-rate model and of a genetic distance (wherein branch lengths are used to determine the probabilities of change) or speciational (wherein changes are only driven by speciation events) model based upon a likelihood-ratio test strongly depended on the sampled trees. Despite these differences in model selection, reconstructions of ancestral character states were strongly correlated to each others across nodes, often at r > 0.9, for all the characters. The Bayesian approach of ancestral character state reconstruction offers, however, a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities. From the distribution of the latter, conclusions on trait evolution can be made in a more satisfactorily way than when a substantial part of the uncertainty of the results is obscured by the focus on a single set of model parameters and associated ancestral states. The reconstructions of ancestral character states in Brachytheciastrum reveal rampant parallel morphological evolution. Most species previously described based on phenetic grounds are thus resolved of polyphyletic origin. Species polyphylly has been increasingly reported among mosses, raising severe reservations regarding current species definition.     

Bayesian reconstruction of ancestral expression of the LEA gene families reveals propagule-derived desiccation tolerance in resurrection plants

Desiccation tolerance is a complex trait that is broadly but infrequently present throughout the evolutionary tree of life. Desiccation tolerance has played a significant role in land plant evolution, in both the vegetative and reproductive life history stages. In the land plants, the late embryogenesis abundant (LEA) gene families are involved in both abiotic stress tolerance and the development of reproductive propagules. They are also a major component of vegetative desiccation tolerance. Phylogenies were estimated for four families of LEA genes from Arabidopsis, Physcomitrella, and the desiccation tolerant plants Tortula ruralis, Craterostigma plantagineum, and Xerophyta humilis. Microarray expression data from Arabidopsis and a subset of the Physcomitrella LEAs were used to estimate ancestral expression patterns in the LEA families and to evaluate alternative hypotheses for the origins of vegetative desiccation tolerance in the flowering plants. The results contradict the idea that vegetative desiccation tolerance in the resurrection angiosperms Craterostigma and Xerophyta arose through the co-option of genes exclusively related to stress tolerance, and support the propagule-derived origin of vegetative desiccation tolerance in the resurrection plants.     

Carotenoids from the crimson and maroon plumages of Old World orioles (Oriolidae)

Recent analyses of the orange, red, and purple plumages of cotingas (Cotingidae) and broadbills (Eurylaimidae) revealed the presence of novel carotenoid molecules, suggesting that the diversity of pigments and the metabolic transformations they undergo are not yet fully understood. Two Old World orioles, the Black-and-Crimson Oriole Oriolus cruentus, and the Maroon Oriole Oriolus traillii, exhibit plumage colors that are similar to those of some cotingas and broadbills. To determine if these oriole plumage colors are produced by the same carotenoids or with other molecules, we used high-performance liquid chromatography (HPLC), mass spectrometry, and chemical analyses. The data show that the bright red feathers of O. cruentus contain a suite of keto-carotenoids commonly found in avian plumages, including canthaxanthin, adonirubin, astaxanthin, papilioerythrinone, and α-doradexanthin. The maroon feathers of O. traillii were found to contain canthaxanthin, α-doradexanthin, and one novel carotenoid, 3′,4-dihydroxy-ε,ε-carotene-3-one, which we have termed “4-hydroxy-canary xanthophyll A.” In this paper we propose the metabolic pathways by which these pigments are formed. This work advances our understanding of the evolution of carotenoid metabolism in birds and the mechanisms by which birds achieve their vivid plumage colorations.     

The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota)

Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions. This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apex of the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex has been highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using Bayesian Markov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrial rDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method for assessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather than on likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood on a posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly different depending on the method used; different methods often assign high confidence to different states at a given node. The two fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similar likelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting an improved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in the Lecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is 12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apex types. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny corresponds well with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae, Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.     

Footprints of selection in the ancestral admixture of a New World Creole cattle breed

Admixed populations represent attractive biological models to study adaptive selection. Originating from several waves of recent introduction from European (EUT), African (AFT) and zebus (ZEB) cattle, New World Creole cattle allow investigating the response to tropical environmental challenges of these three ancestries. We here provide a detailed assessment of their genetic contributions to the Creole breed from Guadeloupe (CGU). We subsequently look for footprints of selection by combining results from tests based on the extent of haplotype homozygosity and the identification of excess/deficiency of local ancestry. To tackle these issues, 140 CGU individuals and 25 Brahman zebus from Martinique were genotyped at 44 057 SNPs. These data were combined to those available on 23 populations representative of EUT, AFT or ZEB. We found average proportions of 26.1%, 36.0% and 37.9% of EUT, AFT and ZEB ancestries in the CGU genome indicating a higher level of African and zebu ancestries than suggested by historical records. We further identified 23 genomic regions displaying strong signal of selection, most of them being characterized by an excess of ZEB local ancestry. Among the candidate gene underlying these regions, several are associated with reproductive functions (RXFP2, PMEPA1, IGFBP3, KDR, PPP1R8, TBXA2R and SLC7A5) and metabolism (PDE1B and CYP46A1). Finally, two genes (CENTD3 and SAMD12) are involved in cellular signalization of immune response. This study illustrates the relevance of admixed populations to identify footprints of selection by combining several tests straightforward to implement on large data sets.     

Characterization of ancestral and derived Y-chromosome haplotypes of New World native populations.

We analyze the allelic polymorphisms in seven Y-specific microsatellite loci and a Y-specific alphoid system with 27 variants (alphah I-XXVII), in a total of 89 Y chromosomes carrying the DYS199T allele and belonging to populations representing Amerindian and Na-Dene linguistic groups. Since there are no indications of recurrence for the DYS199C-->T transition, it is assumed that all DYS199T haplotypes derive from a single individual in whom the C-->T mutation occurred for the first time. We identified both the ancestral founder haplotype, 0A, of the DYS199T lineage and seven derived haplogroups diverging from the ancestral one by one to seven mutational steps. The 0A haplotype (5.7% of Native American chromosomes) had the following constitution: DYS199T, alphah II, DYS19/13, DYS389a/10, DYS389b/27, DYS390/24, DYS391/10, DYS392/14, and DYS393/13 (microsatellite alleles are indicated as number of repeats). We analyzed the Y-specific microsatellite mutation rate in 1,743 father-son transmissions, and we pooled our data with data in the literature, to obtain an average mutation rate of.0012. We estimated that the 0A haplotype has an average age of 22,770 years (minimum 13,500 years, maximum 58,700 years). Since the DYS199T allele is found with high frequency in Native American chromosomes, we propose that 0A is one of the most prevalent founder paternal lineages of New World aborigines.     

What lies beneath: molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea)

The crustacean family Parabathynellidae is an ancient and significant faunal component of subterranean ecosystems. Molecular data were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species diversity of this group within Australia. We also used the resultant phylogenetic framework, in combination with an ancestral state reconstruction (ASR) analysis, to explore the evolution of two key morphological characters (number of segments of the first and second antennae), previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ASR approach also allowed an assessment of whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Sequence data from the mtDNA COI and nDNA 18S rRNA genes were obtained from 32 parabathynellid species (100% of described genera and ~25% of described species) from key groundwater regions across Australia. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. Additionally, ancestral state reconstruction analysis provided evidence for multiple cases of convergent evolution for the two morphological characters evaluated, suggesting that caution needs to be shown when using these characters for elucidating phylogenetic relationships, particularly when there are few morphological characters available for reconstructing relationships. The ancestral state analysis contradicted the conventional view of parabathynellid evolution, which assumes that more simplified taxa (i.e. those with fewer-segmented appendages and setae) are derived and more complex taxa are primitive.     

An experimental test of the contributions and condition dependence of microstructure and carotenoids in yellow plumage coloration

A combination of structural and pigmentary components is responsible for many of the colour displays of animals. Despite the ubiquity of this type of coloration, neither the relative contribution of structures and pigments to variation in such colour displays nor the relative effects of extrinsic factors on the structural and pigment-based components of such colour has been determined. Understanding the sources of colour variation is important because structures and pigments may convey different information to conspecifics. In an experiment on captive American goldfinches Carduelis tristis, we manipulated two parameters, carotenoid availability and food availability, known to affect the expression of carotenoid pigments in a full-factorial design. Yellow feathers from these birds were then analysed in two ways. First, we used full-spectrum spectrometry and high-performance liquid chromatography to examine the extent to which variation in white structural colour and total carotenoid content was associated with variation in colour properties of feathers. The carotenoid content of yellow feathers predicted two colour parameters (principal component 1--representing high values of ultraviolet and yellow chroma and low values of violet-blue chroma-and hue). Two different colour parameters (violet-blue and yellow chroma) from white de-pigmented feathers, as well as carotenoid content, predicted reflectance measurements from yellow feathers. Second, we determined the relative effects of our experimental manipulations on white structural colour and yellow colour. Carotenoid availability directly affected yellow colour, while food availability affected it only in combination with carotenoid availability. None of our manipulations had significant effects on the expression of white structural colour. Our results suggest that the contribution of microstructures to variation in the expression of yellow coloration is less than the contribution of carotenoid content, and that carotenoid deposition is more dependent on extrinsic variability than is the production of white structural colour.     

Rate heterogeneity, ancestral character state reconstruction, and the evolution of limb morphology in Lerista (Scincidae, Squamata)

Rates of phenotypic evolution derive from numerous interrelated processes acting at varying spatial and temporal scales and frequently differ substantially among lineages. Although current models employed in reconstructing ancestral character states permit independent rates for distinct types of transition (forward and reverse transitions and transitions between different states), these rates are typically assumed to be identical for all branches in a phylogeny. In this paper, I present a general model of character evolution enabling rate heterogeneity among branches. This model is employed in assessing the extent to which the assumption of uniform transition rates affects reconstructions of ancestral limb morphology in the scincid lizard clade Lerista and, accordingly, the potential for rate variability to mislead inferences of evolutionary patterns. Permitting rate variation among branches significantly improves model fit for both the manus and the pes. A constrained model in which the rate of digit acquisition is assumed to be effectively zero is strongly supported in each case; when compared with a model assuming unconstrained transition rates, this model provides a substantially better fit for the manus and a nearly identical fit for the pes. Ancestral states reconstructed assuming the constrained model imply patterns of limb evolution differing significantly from those implied by reconstructions for uniform-rate models, particularly for the pes; whereas ancestral states for the uniform-rate models consistently entail the reacquisition of pedal digits, those for the model incorporating among-lineage rate heterogeneity imply repeated, unreversed digit loss. These results indicate that the assumption of identical transition rates for all branches in a phylogeny may be inappropriate in modeling the evolution of phenotypic traits and emphasize the need for careful evaluation of phylogenetic tests of Dollo's law.     

Intraspecific variability and timing in ancestral ecology reconstruction: a test case from the cape flora

Thamnochortus (ca. 32 species) is an ecologically diverse genus of Restionaceae. Restionaceae comprise a major component of the southern African Cape flora, wherein eco-diversification might have been important in the generation of high levels of species richness. In an attempt to reconstruct the macroecological history of Thamnochortus, it was found that standard procedures for character state optimization make two inappropriate assumptions. The first is that ancestors are monomorphic (i.e., ecologically uniform) and the second is that eco-diversification follows, or is slower than, lineage diversification. We demonstrate a variety of coding schemes with which the assumption of monomorphy can be avoided. For unordered discrete ecological characters, presence coding and generalized frequency coding (GFC) are suboptimal because they occasionally yield illogical assignments of no state to ancestors. Polymorphism coding or use of the program DIVA are preferable in this respect but are applicable only with parsimony. For continuous eco-characters (e.g., a rainfall gradient, where individual species occur in ranges), GFC and MaxMin coding provide equally valid solutions to optimizing ranges with parsimony. However, MaxMin can be extended to likelihood approaches and is therefore preferable. With respect to rates and timing, all algorithms currently employed for ancestral ecology reconstruction bias toward slow rates of eco-diversification relative to lineage diversification. An alternative to this bias is provided by DIVA, which biases toward accelerated rates of eco-diversification and thus inferences of ecology-driven speciation. We see no way of choosing between these biases; however, phylogeneticists should be aware of them. Applying these methods to Thamnochortus, we find there to be important differences in details, yet general congruence, regarding the historical ecology of this clade. We infer the most recent common ancestor of Thamnochortus to have been a post-fire resprouting species distributed on rocky, well-drained, sandstone-derived soils at lower-middle elevations, in regions of moderate levels of yearly (primarily winter) rainfall. This species would have been distributed in habitats much like those of the southwestern Cape mountains today. Major ecological trends include shifts to lower rainfall regimes and shifts from sandstone to limestone-derived alkaline soils at lower altitudes.     

Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene

Background  

Alternative splicing of mutually exclusive exons is an important mechanism for increasing protein diversity in eukaryotes. The insect Mhc (myosin heavy chain) gene produces all different muscle myosins as a result of alternative splicing in contrast to most other organisms of the Metazoa lineage, that have a family of muscle genes with each gene coding for a protein specialized for a functional niche.     

A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages

Island systems have long been useful models for understanding lineage diversification in a geographic context, especially pertaining to the importance of dispersal in the origin of new clades. Here we use a well-resolved phylogeny of the flowering plant genus Cyrtandra (Gesneriaceae) from the Pacific Islands to compare four methods of inferring ancestral geographic ranges in islands: two developed for character-state reconstruction that allow only single-island ranges and do not explicitly associate speciation with range evolution (Fitch parsimony [FP; parsimony-based] and stochastic mapping [SM; likelihood-based]) and two methods developed specifically for ancestral range reconstruction, in which widespread ranges (spanning islands) are integral to inferences about speciation scenarios (dispersal-vicariance analysis [DIVA; parsimony-based] and dispersal-extinction-cladogenesis [DEC; likelihood-based]). The methods yield conflicting results, which we interpret in light of their respective assumptions. FP exhibits the least power to unequivocally reconstruct ranges, likely due to a combination of having flat (uninformative) transition costs and not using branch length information. SM reconstructions generally agree with a prior hypothesis about dispersal-driven speciation across the Pacific, despite the conceptual mismatch between its character-based model and this mode of range evolution. In contrast with narrow extant ranges for species of Cyrtandra, DIVA reconstructs broad ancestral ranges at many nodes. DIVA results also conflict with geological information on island ages; we attribute these conflicts to the parsimony criterion not considering branch lengths or time, as well as vicariance being the sole means of divergence for widespread ancestors. DEC analyses incorporated geological information on island ages and allowed prior hypotheses about range size and dispersal rates to be evaluated in a likelihood framework and gave more nuanced inferences about range evolution and the geography of speciation than other methods tested. However, ancestral ranges at several nodes could not be conclusively resolved, due possibly to uncertainty in the phylogeny or the relative complexity of the underlying model. Of the methods tested, SM and DEC both converge on plausible hypotheses for area range histories in Cyrtandra, due in part to the consideration of branch lengths and/or timing of events. We suggest that DEC model-based methods for ancestral range inference could be improved by adopting a Bayesian SM approach, in which stochastic sampling of complete geographic histories could be integrated over alternative phylogenetic topologies. Likelihood-based estimates of ancestral ranges for Cyrtandra suggest a major dispersal route into the Pacific through the islands of Fiji and Samoa, motivating future biogeographic investigation of this poorly known region.     

Extraordinary resistance to insecticides reveals exotic Q biotype of Bemisia tabaci in the New World

A strain of the whitefly Bemisia tabaci (Gennadius) possessing unusually high levels of resistance to a wide range of insecticides was discovered in 2004 in the course of routine resistance monitoring in Arizona. The multiply resistant insects, collected from poinsettia (Euphorbia pulcherrima Willd. ex Klotzsch) plants purchased at a retail store in Tucson, were subjected to biotype analysis in three laboratories. Polyacrylamide gel electrophoresis of naphthyl esterases and sequencing of the mitochondrial cytochrome oxidase I gene (780 bp) confirmed the first detection of the Q biotype of B. tabaci in the New World. This U.S. Q biotype strain, referred to as Poinsettia'04, was highly resistant to two selective insect growth regulators, pyriproxyfen and buprofezin, and to mixtures of fenpropathrin and acephate. It was also unusually low in susceptibility to the neonicotinoid insecticides imidacloprid, acetamiprid, and thiamethoxam, relative to B biotype whiteflies. In 100 collections of whiteflies made in Arizona cotton (Gossypium spp.), vegetable, and melon (Cucumis melo L.) fields from 2001 to 2005, no Q biotypes were detected. Regions of the United States that were severely impacted by the introduction of the B biotype of B. tabaci in the 1980s would be well advised to promote measures that limit movement of the Q biotype from controlled environments into field systems and to formulate alternatives for managing this multiply-resistant biotype, in the event that it becomes more widely distributed.     

Robustness of ancestral state estimates: evolution of life history strategy in ichneumonoid parasitoids

We test hypotheses for the evolution of a life history trait among a group of parasitoid wasps (Hymenoptera: Ichneumonoidea), namely, the transition among koinobiont parasitoids (parasitoids whose hosts continue development after oviposition) between attacking exposed hosts and attacking hosts that are concealed within plant tissue. Using a range of phylogeny estimates based on 28S rDNA sequences, we use maximum parsimony (MP) and maximum likelihood (ML) methods to estimate the ancestral life history traits for the main clades in which both traits occur (using the programs MacClade and Discrete, respectively). We also assess the robustness of these estimates; for MP, we use step matrices in PAUP* to find the minimum weight necessary to reverse estimates or make them ambiguous, and for ML, we measure the differences in likelihood after fixing the ancestral nodes at the alternative states. We also measure the robustness of the MP ancestral state estimate against uncertainties in the phylogeny estimate, manipulating the most-parsimonious tree in MacClade to find the shortest suboptimal tree in which the ancestral state estimate is reversed or made ambiguous. Using these methods, we find strong evidence supporting two transitions among koinobiont Ichneumonoidea: (1) to attacking exposed hosts in a clade consisting of the Helconinae and related subfamilies, and (2) the reverse transition in a clade consisting of the Euphorinae and related subfamilies. In exploring different methods of analyzing variable-length DNA sequences, we found that direct optimization with POY gave some clearly erroneous results that had a profound effect on the overall phylogeny estimate. We also discuss relationships within the superfamily and expand the Mesostoinae to include all the gall-associated braconids that form the sister group of the Aphidiinae.