FInCH: FIJI plugin for automated and scalable whole-image analysis of protein expression and cell morphology.

Study of morphogenesis and its regulation requires analytical tools that enable simultaneous assessment of processes operating at cellular level, such as synthesis of transcription factors (TF), with their effects at the tissue scale. Most current studies conduct histological, cellular and immunochemical (IHC) analyses in separate steps, introducing inevitable biases in finding and alignment of areas of interest at vastly distinct scales of organization, as well as image distortion associated with image repositioning or file modifications. These problems are particularly severe for longitudinal analyses of growing structures that change size and shape.

Turning induced plasticity into refined adaptations during range expansion.

Robustness against environmental fluctuations within an adaptive state should preclude exploration of new adaptive states when the environment changes. Here, we study transitions between adaptive associations of feather structure and carotenoid uptake to understand how robustness and evolvability can be reconciled. We show that feather modifications induced by unfamiliar carotenoids during a range expansion are repeatedly converted into precise coadaptations of feather development and carotenoid accommodation as populations persist in a region.

Cycles of external dependency drive evolution of avian carotenoid networks.

All organisms depend on input of exogenous compounds that cannot be internally produced. Gain and loss of such dependencies structure ecological communities and drive species' evolution, yet the evolution of mechanisms that accommodate these variable dependencies remain elusive. Here, we show that historical cycles of gains and losses of external dependencies in avian carotenoid-producing networks are linked to their evolutionary diversification.

Extensive phenotypic diversification coexists with little genetic divergence and a lack of population structure in the White Wagtail subspecies complex (Motacilla alba).

Geographically clustered phenotypes often demonstrate consistent patterns in molecular markers, particularly mitochondrial DNA (mtDNA) traditionally used in phylogeographic studies. However, distinct evolutionary trajectories among traits and markers can lead to their discordance. First, geographic structure in phenotypic traits and nuclear molecular markers can be co-aligned but inconsistent with mtDNA (mito-nuclear discordance).

Evolutionary transitions in controls reconcile adaptation with continuity of evolution.

Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits.

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network.

Emergent buffering balances evolvability and robustness in the evolution of phenotypic flexibility.

Evolution of adaptive phenotypic flexibility requires a system that can dynamically restore and update a functional phenotype in response to environmental change. The architecture of such a system evolves under the conflicting demands of versatility and robustness, and resolution of these demands should be particularly evident in organisms that require external inputs for reiterative trait production within a generation, such as in metabolic networks that underlie yearly acquisition of diet-dependent coloration in birds. Here, we show that a key structural feature of carotenoid networks-redundancy of biochemical pathways-enables these networks to translate variable environmental inputs into consistent phenotypic outcomes.

Most Colorful Example of Genetic Assimilation? Exploring the Evolutionary Destiny of Recurrent Phenotypic Accommodation.

Evolution of adaptation requires both generation of novel phenotypic variation and retention of a locally beneficial subset of this variation. Such retention can be facilitated by genetic assimilation, the accumulation of genetic and molecular mechanisms that stabilize induced phenotypes and assume progressively greater control over their reliable production. A particularly strong inference into genetic assimilation as an evolutionary process requires a system where it is possible to directly evaluate the extent to which an induced phenotype is progressively incorporated into preexisting developmental pathways.

Structuring evolution: biochemical networks and metabolic diversification in birds.

Background: Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds.

The Landscape of Evolution: Reconciling Structural and Dynamic Properties of Metabolic Networks in Adaptive Diversifications.

The network of the interactions among genes, proteins, and metabolites delineates a range of potential phenotypic diversifications in a lineage, and realized phenotypic changes are the result of differences in the dynamics of the expression of the elements and interactions in this deterministic network. Regulatory mechanisms, such as hormones, mediate the relationship between the structural and dynamic properties of networks by determining how and when the elements are expressed and form a functional unit or state. Changes in regulatory mechanisms lead to variable expression of functional states of a network within and among generations.

Evolution of long-term coloration trends with biochemically unstable ingredients.

The evolutionarily persistent and widespread use of carotenoid pigments in animal coloration contrasts with their biochemical instability. Consequently, evolution of carotenoid-based displays should include mechanisms to accommodate or limit pigment degradation. In birds, this could involve two strategies: (i) evolution of a moult immediately prior to the mating season, enabling the use of particularly fast-degrading carotenoids and (ii) evolution of the ability to stabilize dietary carotenoids through metabolic modification or association with feather keratins.

Causes of Discordance between Allometries at and above Species Level: An Example with Aquatic Beetles.

Covariation among organismal traits is nearly universal, occurring both within and among species (static and evolutionary allometry, respectively). If conserved developmental processes produce similarity in static and evolutionary allometry, then when species differ in development, it should be expressed in discordance between allometries. Here, we investigate whether rapidly evolving developmental processes result in discordant static and evolutionary allometries attributable to trade-offs in resource acquisition, allocation, or growth across 30 species of aquatic beetles.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification.

Background: Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment.

Epigenetic resolution of the 'curse of complexity' in adaptive evolution of complex traits.

The age of most genes exceeds the longevity of their genomic and physiological associations by many orders of magnitude. Such transient contexts modulate the expression of ancient genes to produce currently appropriate and often highly distinct developmental and functional outcomes. The efficacy of such adaptive modulation is diminished by the high dimensionality of complex organisms and associated vast areas of neutrality in their genotypic and developmental networks (and, thus, weak natural selection).

"Homeostatic hitchhiking": a mechanism for the evolutionary retention of complex adaptations.

The complexity of organismal organization channels and accommodates novel genomic and developmental modifications. Here, I extend this perspective to suggest that emergent processes that dominate homeostasis-co-option, re-use, and recombination of accumulated elements-can create configurations and dependencies among these elements that strongly reduce the number of evolutionary steps needed for the evolution of precise novel adaptations. Evolutionary retention and environmental matching of such configurations are further facilitated when they include elements of homeostasis that are responsive to particular environmental cues.

Gene loss, thermogenesis, and the origin of birds.

Compared to related taxa, birds have exceptionally enlarged and diversified skeletal muscles, features that are closely associated with skeletal diversification and are commonly explained by a diversity of avian ecological niches and locomotion types. The thermogenic muscle hypothesis (TMH) for the origin of birds proposes that such muscle hyperplasia and the associated skeletal innovations are instead the consequence of the avian clade originating from an ancestral population that underwent several successive episodes of loss of genes associated with thermogenesis, myogenesis, and skeletogenesis. Direct bird ancestors met this challenge with a combination of behavioral strategies (e.

Developmental integration of feather growth and pigmentation and its implications for the evolution of diet-derived coloration.

Variation in avian coloration is produced by coordinated pigmentation of thousands of growing feathers that vary in shape and size. Although the functional consequences of avian coloration are frequently studied, little is known about its developmental basis, and, specifically, the rules that link feather growth to pigment uptake and synthesis. Here, we combine biochemical, modeling, and morphometric techniques to examine the developmental basis of feather pigmentation in house finches (Carpodacus mexicanus)--a species with extensive variation in both growth dynamics of ornamental feathers and their carotenoid pigmentation.

Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology.

In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed.

Developmental plasticity links local adaptation and evolutionary diversification in foraging morphology.

Developmental plasticity is thought to reconcile the constraining role of natural selection in maintaining local adaptation with evolutionary diversification under novel conditions, but empirical documentations are rare. In vertebrates, growth and development of bones is partially guided by contractions of attached musculature and such muscle activity changes progressively through embryonic development from sporadic motility to direct functional effects. In species with short generation times, delayed skull maturation extends the guiding effects of muscle activity on formation of foraging morphology into adulthood, providing an opportunity to directly examine the links between plasticity of bone development, ecological adaptations, and evolutionary diversification in foraging morphology.

Structure of social networks in a passerine bird: consequences for sexual selection and the evolution of mating strategies.

The social environment is a critical determinant of fitness and, in many taxa, is shaped by an individual's behavioral discrimination among social contexts, suggesting that animals can actively influence the selection they experience. In competition to attract females, males may modify sexual selection by choosing social environments in which they are more attractive relative to rivals. Across the population, such behaviors should influence sexual selection patterns by altering the relationship between male mating success and sexual ornament elaboration.

The beak of the other finch: coevolution of genetic covariance structure and developmental modularity during adaptive evolution.

The link between adaptation and evolutionary change remains the most central and least understood evolutionary problem. Rapid evolution and diversification of avian beaks is a textbook example of such a link, yet the mechanisms that enable beak's precise adaptation and extensive adaptability are poorly understood. Often observed rapid evolutionary change in beaks is particularly puzzling in light of the neo-Darwinian model that necessitates coordinated changes in developmentally distinct precursors and correspondence between functional and genetic modularity, which should preclude evolutionary diversification.

Isolation and characterization of 17 microsatellite loci for the house finch (Carpodacus mexicanus).

The house finch (Carpodacus mexicanus) has emerged recently as a model species in studies of sexual selection, reproductive physiology, population genetics, and epizootic disease ecology. Here we describe 17 highly polymorphic microsatellite loci for this species. In a sample of 36 individuals, we observed an average of 16 alleles per locus and heterozygosity ranged from 0.

Parental effects in ecology and evolution: mechanisms, processes and implications.

As is the case with any metaphor, parental effects mean different things to different biologists--from developmental induction of novel phenotypic variation to an evolved adaptation, and from epigenetic transference of essential developmental resources to a stage of inheritance and ecological succession. Such a diversity of perspectives illustrates the composite nature of parental effects that, depending on the stage of their expression and whether they are considered a pattern or a process, combine the elements of developmental induction, homeostasis, natural selection, epigenetic inheritance and historical persistence. Here, we suggest that by emphasizing the complexity of causes and influences in developmental systems and by making explicit the links between development, natural selection and inheritance, the study of parental effects enables deeper understanding of developmental dynamics of life cycles and provides a unique opportunity to explicitly integrate development and evolution.

Evolutionary significance of phenotypic accommodation in novel environments: an empirical test of the Baldwin effect.

When faced with changing environments, organisms rapidly mount physiological and behavioural responses, accommodating new environmental inputs in their functioning. The ubiquity of this process contrasts with our ignorance of its evolutionary significance: whereas within-generation accommodation of novel external inputs has clear fitness consequences, current evolutionary theory cannot easily link functional importance and inheritance of novel accommodations. One hundred and twelve years ago, J.