Tapping the woodpecker tree for evolutionary insight

Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis

The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.

Chromosome-level genome assembly of the European green woodpecker Picus viridis

The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the P. viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers. Five historical and seven contemporary samples have been resequenced and may give insights on the population history of this species.

Evolution of Plumage Patterns in a Pattern Morphospace: A Phylogenetic Analysis of Melanerpine Woodpeckers

AbstractPlumage patterns of melanerpine (Melanerpes-Sphyrapicus) woodpeckers are strikingly diverse. Understanding the evolution and function of this diversity is challenging because of the difficulty of quantifying plumage patterns. We use a three-dimensional space to characterize the evolution of melanerpine achromatic plumage patterns. The axes of the space are three pattern features (spatial frequency, orientation, and contrast) quantified using two-dimensional fast Fourier transformation of museum specimen images. Mapping plumage in pattern space reveals differences in how species and subclades occupy the space. To quantify these differences, we derive two new measures of pattern: pattern diversity (diversity across plumage patches within a species) and pattern uniqueness (divergence of patterns from those of other species). We estimate that the melanerpine ancestor had mottled plumage and find that pattern traits across patches and subclades evolve at different rates. We also find that smaller species are more likely to display horizontal face patterning. We promote pattern spaces as powerful tools for investigating animal pattern evolution.

Convergent genomic signatures of local adaptation across a continental-scale environmental gradient

Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.

Feather function and the evolution of birds

The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.

Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow

Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.

A single residue confers selective loss of sugar sensing in wrynecks

Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions.^1-3 Although receptor sensitivities can be highly contingent on changes occurring early in a lineage's evolutionary history,⁴ subsequent shifts in a species' behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities.^5-7 Neither the extent to which sensory reversion occurs nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds.^8,9 Our analyses show that, similar to hummingbirds¹⁰ and songbirds,⁴ the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.

Correlated evolution between colour conspicuousness and drum speed in woodpeckers

Sexual selection drives the evolution of many spectacular animal displays that we see in nature. Yet, how selection combines and elaborates different signal traits remains unclear. Here, we investigate this issue by testing for correlated evolution between head plumage colour and drumming behaviour in woodpeckers. These signals function in the context of mate choice and male-male competition, and they may appear to a receiver as a single multimodal display. We test for such correlations in males of 132 species using phylogenetic linear models, while considering the effect of habitat. We find that the plumage chromatic contrast is positively correlated with the speed of the drum, supporting the idea that species evolving more conspicuous plumage on their head also evolve faster drum displays. By contrast, we do not find evidence of correlated evolution between drum speed and head colour diversity, size of the head's red patch, or extent of the plumage achromatic contrast. Drum length was not correlated with any of the plumage coloration metrics. Lastly, we find no evidence that habitat acts as a strong selective force driving the evolution of head coloration or drumming elaboration. Coevolution between different signal modalities is therefore complex, and probably depends on the display components in question.

Genetic diversity and spatial genetic structure support the specialist-generalist variation hypothesis in two sympatric woodpecker species

Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.

The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus

Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.

Evolutionary and Biomechanical Basis of Drumming Behavior in Woodpeckers

Understanding how and why behavioral traits diversify during the course of evolution is a longstanding goal of organismal biologists. Historically, this topic is examined from an ecological perspective, where behavioral evolution is thought to occur in response to selection pressures that arise through different social and environmental factors. Yet organismal physiology and biomechanics also play a role in this process by defining the types of behavioral traits that are more or less likely to arise. Our paper explores the interplay between ecological, physiological, and mechanical factors that shape the evolution of an elaborate display in woodpeckers called the drum. Individuals produce this behavior by rapidly hammering their bill on trees in their habitat, and it serves as an aggressive signal during territorial encounters. We describe how different components of the display—namely, speed (bill strikes/beats sec–1), length (total number of beats), and rhythm—differentially evolve likely in response to sexual selection by male-male competition, whereas other components of the display appear more evolutionarily static, possibly due to morphological or physiological constraints. We synthesize research related to principles of avian muscle physiology and ecology to guide inferences about the biomechanical basis of woodpecker drumming. Our aim is to introduce the woodpecker as an ideal study system to study the physiological basis of behavioral evolution and how it relates to selection born through different ecological factors.

Using Integrative Biology to Infer Adaptation from Comparisons of Two (or a Few) Species

AbstractPhylogenetic comparative methods represent a major advance in integrative and comparative biology and have allowed researchers to rigorously test for adaptation in a macroevolutionary framework. However, phylogenetic comparative methods require trait data for many species, which is impractical for certain taxonomic groups and trait types. We propose that the philosophical principle of severity can be implemented in an integrative framework to generate strong inference of adaptation in studies that compare only a few populations or species. This approach requires (1) ensuring that the study system contains species that are relatively closely related; (2) formulating a specific, clear, overarching hypothesis that can be subjected to integrative testing across levels of biological organization (e.g., ecology, behavior, morphology, physiology, and genetics); (3) collecting data that avoid statistical underdetermination and thus allow severe tests of hypotheses; and (4) systematically refining and refuting alternative hypotheses. Although difficult to collect for more than a few species, detailed, integrative data can be used to differentiate among several potential agents of selection. In this way, integrative studies of small numbers of closely related species can complement and even improve on broadscale phylogenetic comparative studies by revealing the specific drivers of adaptation.

Evolution of communication signals and information during species radiation

Communicating species identity is a key component of many animal signals. However, whether selection for species recognition systematically increases signal diversity during clade radiation remains debated. Here we show that in woodpecker drumming, a rhythmic signal used during mating and territorial defense, the amount of species identity information encoded remained stable during woodpeckers' radiation. Acoustic analyses and evolutionary reconstructions show interchange among six main drumming types despite strong phylogenetic contingencies, suggesting evolutionary tinkering of drumming structure within a constrained acoustic space. Playback experiments and quantification of species discriminability demonstrate sufficient signal differentiation to support species recognition in local communities. Finally, we only find character displacement in the rare cases where sympatric species are also closely related. Overall, our results illustrate how historical contingencies and ecological interactions can promote conservatism in signals during a clade radiation without impairing the effectiveness of information transfer relevant to inter-specific discrimination.

Selection for Rhythm as a Trigger for Recursive Evolution in the Elaborate Display System of Woodpeckers

Evolution is never truly predictable, in part because the process of selection is recursive: it operates on its own output to generate historical contingencies, so emergent traits can reshape how others evolve in the future. Studies rarely attempt to directly trace how recursion underlies present-day phenotypic pattern on a macroevolutionary basis. To address this gap, we examined how different selection regimes-each operating on a different timescale-guide the evolution of the woodpecker drum display. Approximately 200 species drum with distinctive speed and length, which are important for territorial competition. We discovered remarkable variation in drum rhythm, with some species drumming at constant rates and others changing speed along a range of mathematical functions. Rhythm undergoes divergent character displacement among sympatric sister species, a process that wanes as other reproductive boundaries emerge over time. Tracing the recursive effects of this process, we found that modifying rhythm may then potentiate or constrain speed/length elaboration. Additionally, increased sexual size dimorphism predicts the emergence of rhythms associated with constrained evolutionary rates of speed/length, implying that selection can also constrain itself. Altogether, our findings illustrate how recursion introduces contingencies that allow diverse phenotypes to arise from similar selection regimes.

Ecological and geographical overlap drive plumage evolution and mimicry in woodpeckers

Organismal appearances are shaped by selection from both biotic and abiotic drivers. For example, Gloger's rule describes the pervasive pattern that more pigmented populations are found in more humid areas. However, species may also converge on nearly identical colours and patterns in sympatry, often to avoid predation by mimicking noxious species. Here we leverage a massive global citizen-science database to determine how biotic and abiotic factors act in concert to shape plumage in the world's 230 species of woodpeckers. We find that habitat and climate profoundly influence woodpecker plumage, and we recover support for the generality of Gloger's rule. However, many species exhibit remarkable convergence explained neither by these factors nor by shared ancestry. Instead, this convergence is associated with geographic overlap between species, suggesting occasional strong selection for interspecific mimicry.

Multiple and Independent Phases of Transposable Element Amplification in the Genomes of Piciformes (Woodpeckers and Allies)

The small and conserved genomes of birds are likely a result of flight-related metabolic constraints. Recombination-driven deletions and minimal transposable element (TE) expansions have led to continually shrinking genomes during evolution of many lineages of volant birds. Despite constraints of genome size in birds, we identified multiple waves of amplification of TEs in Piciformes (woodpeckers, honeyguides, toucans, and barbets). Relative to other bird species’ genomic TE abundance (< 10% of genome), we found ∼17–30% TE content in multiple clades within Piciformes. Several families of the retrotransposon superfamily chicken repeat 1 (CR1) expanded in at least three different waves of activity. The most recent CR1 expansions (∼4–7% of genome) preceded bursts of diversification in the woodpecker clade and in the American barbets + toucans clade. Additionally, we identified several thousand polymorphic CR1 insertions (hundreds per individual) in three closely related woodpecker species. Woodpecker CR1 insertion polymorphisms are maintained at lower frequencies than single nucleotide polymorphisms indicating that purifying selection is acting against additional CR1 copies and that these elements impose a fitness cost on their host. These findings provide evidence of large scale and ongoing TE activity in avian genomes despite continual constraint on genome size.