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bioRxiv2024

The distribution of clade size in a coalescent diversification model

Characterizing the patterns and determinants of biological diversity is a central aim of evolutionary biology. Doing so requires developing expectations for clade size, the relationship between the number of species in a clade and its age, for standard diversification models, such as the coalescent or birth-death process. These expectations are necessary for identifying diversity outliers, specious or depauperate clades in the macroevolutionary context or transmission clusters of particular or little public health concern in the epidemiological context, and for testing alternative diversification hypotheses. Here, we derive a closed-form expression for the distribution of clade sizes under the widely used Kingman coalescent diversification model and extend the results to allow the number of niches (the effective population size) to vary through time. This result complements analogous results for the birth-death model in that it provides expectations for the joint distribution of clade sizes for a case where diversification is strongly density-dependent.

genetics↗

bioRxiv2018

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

Myxoma virus (MYXV) has been evolving in a novel host species - European rabbits - in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of the M005L/R gene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution.\n\nIMPORTANCEThe co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural experiments in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.

evolutionary biology↗

bioRxiv2016

Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms

A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance. Because of this relationship, many theories invoke a role for population size in the evolution of complexity. Such theories are difficult to test empirically because of the time required for the evolution of complexity in biological populations. Here, we used digital experimental evolution to test whether large or small asexual populations tend to evolve greater complexity. We find that both small and large--but not intermediate-sized--populations are favored to evolve larger genomes, which provides the opportunity for subsequent increases in phenotypic complexity. However, small and large populations followed different evolutionary paths towards these novel traits. Small populations evolved larger genomes by fixing slightly deleterious insertions, while large populations fixed rare beneficial insertions that increased genome size. These results demonstrate that genetic drift can lead to the evolution of complexity in small populations and that purifying selection is not powerful enough to prevent the evolution of complexity in large populations.\n\nAuthor SummarySince the early days of theoretical population genetics. scientists have debated the role of population size in shaping evolutionary dynamics. Do large populations possess an evolutionary advantage towards complexity due to the strength of natural selection in these populations? Or do small populations have the advantage, as genetic drift allows for the exploration of fitness landscapes inaccessible to large populations? There are many theories that predict whether large or small populations-those with strong selection or those with strong drift-should evolve the greatest complexity. Here, we use digital experimental evolution to examine the interplay between population size and the evolution of complexity. We found that genetic drift could lead to increased genome size and phenotypic complexity in very small populations. However, large populations also evolved similar large genomes and complexity. Small populations evolved larger genomes through the fixation of slightly deleterious insertions, while large populations utilized rare beneficial insertions. Our results suggest that both strong drift and strong selection can allow populations to evolve similar complexity, but through different evolutionary trajectories.

Evolutionary Biology↗

bioRxiv2020

Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

O_LIDespite the importance of gene function to evolutionary biology, the applicability of comparative methods to gene function is poorly known. A specific case which has crystalized methodological questions is the "ortholog conjecture", the hypothesis that function evolves faster after duplication (i.e., in paralogs), and conversely is conserved between orthologs. Since the mode of functional evolution after duplication is not well known, we investigate under which reasonable evolutionary scenarios phylogenetic independent contrasts or pairwise comparisons can recover a putative signal of different functional evolution between orthologs and paralogs. C_LIO_LIWe investigate three different simulation models, which represent reasonable but simplified hypotheses about the evolution of a gene function trait. These are time dependent trait acceleration, correlated changes in rates of both sequence and trait evolution, and asymmetric trait jump. For each model we tested phylogenetic independent contrasts and an improved pairwise comparison method which accounts for interactions between events and node age. C_LIO_LIBoth approaches lose power to detect the trend of functional evolution when the functional trait accelerates for a long time following duplication for trees with many duplications, with better power of phylogenetic contrasts under intermediate scenarios. Concomitant increase in evolutionary rates of sequence and of trait after duplication can lead to both an incorrect rejection of the null under null simulations of trait evolution, and a false rejection of the ortholog conjecture under ortholog conjecture simulations, by phylogenetic independent contrasts. Improved pairwise comparisons are robust to this bias. Both approaches perform equally well under rapid shifts in traits. C_LIO_LIConsidering our ignorance of gene function evolution, and the potential for bias under simple models, we recommend methodological pluralism in studying gene family evolution. Functional phylogenomics is complex and results supported by only one method should be treated with caution. C_LI

evolutionary biology↗

bioRxiv2023

Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila

Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila, many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila. We first inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to -amanitin and found that six of these species could develop on diet with toxin. Third, we examined fly development on a diet containing a natural mix of toxins extracted from the Death Cap Amanita phalloides mushroom. Both tolerant and susceptible species developed on diet with this mix, though tolerant species survived at significantly higher concentrations. Finally, we asked how cyclopeptide tolerance might have evolved across the immigrans-tripunctata radiation and inferred that toxin tolerance was ancestral and subsequently lost multiple times. Our results suggest the evolutionary history of cyclopeptide tolerance is complex, and simply describing this trait as present or absent does not fully capture the occurrence or impact on this adaptive radiation. More broadly, the evolution of novelty can be more complex than previously thought, and that accurate descriptions of such novelties are critical in studies examining their evolution.

evolutionary biology↗

bioRxiv2026

Cryptic diversification proceeds despite historical and contemporary hybridization in Patagonian ants

Understanding how independently evolving lineages arise despite ongoing gene flow remains a central question in evolutionary biology. Although genomic studies increasingly suggest that hybridization can accompany diversification, empirical evidence from ecologically dominant insect groups remains limited. Here, we present the first population-scale phylogenomic analysis of Patagonian ants, sampling Dorymyrmex across approximately 450,000 km2. Using genome-wide SNPs, coalescent phylogenetics, phylogenetic networks, demographic modelling, species delimitation, and genome scans, we reconstruct the evolutionary history of this widespread genus. We discovered extensive cryptic diversity with strong genomic differentiation and detected both recent and historical hybridization, demonstrating that substantial genomic divergence accumulated despite recurrent gene flow events. Genome scans further identify candidate loci associated with adaptation to Patagonias contrasting environments, suggesting that ecological divergence contributed to lineage diversification. Our results show that cryptic diversification can proceed despite recurrent gene flow, supporting hybridization as an integral component of the diversification process. More broadly, this study illustrates how genome-scale data can reveal hidden biodiversity and the evolutionary processes shaping it in ecologically important but genomically understudied taxa.

evolutionary biology↗

bioRxiv2022

Lifetime reproductive success is an imprecise but largely unbiased predictor of long-term genetic contribution in historical humans

An individuals lifetime reproductive success (LRS) measures its realised genetic contributions to the next generation, but how well does it predict these over longer periods? Here we use human genealogical data to estimate expected individual genetic contributions (IGC) and quantify the degree to which LRS, relative to other fitness proxies, predicts IGC over longer periods in natural populations. This allows an identification of the life-history stages that are most important in shaping variation in IGC. We use historical genealogical data from two non-isolated local populations in Switzerland to estimate the stabilised IGC for 2,230 individuals ~10 generations after they were born. We find that LRS explains 30% less variation in IGC than the best predictor of IGC, the number of grandoffspring. However, albeit less precise than the number of grandoffspring, we show that LRS does provide an unbiased prediction of IGC and overall predicts IGC better than lifespan and similarly when accounting for offspring survival to adulthood. Overall, our findings demonstrate the value of human genealogy data to evolutionary biology and showing that reproduction - more than lifespan or offspring survival - impacts the long-term genetic contributions of historic humans, even in a population with appreciable migration.

evolutionary biology↗

bioRxiv2023

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

evolutionary biology↗

bioRxiv2020

Horizontal gene transfer-mediated bacterial strain variation affects host fitness

How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. We tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS). Leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions, we pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). We suggest that HGT might contribute to microbiome flexibility and speculate that it can also more generally contribute to host adaptation.

evolutionary biology↗

bioRxiv2021

Understanding the Evolution of Nutritive Taste in Animals: Insights from Biological Stoichiometry and Nutritional Geometry

A major conceptual gap in taste biology is the lack of a general framework for understanding the evolution of different taste modalities among animal species. We turn to two complementary nutritional frameworks, biological stoichiometry theory and nutritional geometry, to develop hypotheses for the evolution of different taste modalities in animals. We describe how the attractive tastes of Na, Ca, P, N and C containing compounds are consistent with principles of both frameworks based on their shared focus on nutritional imbalances and consumer homeostasis. Specifically, we suggest that the evolution of multiple nutritive taste modalities can be predicted by identifying individual elements that are typically more concentrated in the tissues of animals than plants. Additionally, we discuss how consumer homeostasis can inform our understanding of why some taste compounds (i.e., Na, Ca and P salts) can be either attractive or aversive depending on concentration. We also discuss how these complementary frameworks can help to explain the phylogenetic distribution of different taste modalities and improve our understanding of the mechanisms that lead to loss of taste capabilities in some animal lineages. The ideas presented here will stimulate research that bridges the fields of evolutionary biology, sensory biology and ecology.

evolutionary biology↗

bioRxiv2026

Mite Genome Miniaturization: Assembly of the biological control agent Floracarus perrepae reveals dynamic genome evolution in eriophyoid mites

The eriophyoid mites (Acari: Eriophyoidea) represent an extreme case of genome streamlining, with genomes averaging just 32Mb, among the smallest of all animals. This clade of mites is highly diverse with more than 4000 species. Their morphologies are specialized for feeding on their host plants, including a simplified worm-like body plan with just two pairs of legs and modified mouth parts that can induce the formation of galls or plant deformities during feeding. Their generally strong host affinities make eriophyoid mites appealing for use as biological control agents, although their short generation times and small genomes could facilitate rapid evolution and impact their efficacy in management programs. Here, we sequenced the genome of the biological control mite Floracarus perrepae, producing a highly contiguous genome totalling just 23.1 Mb, among the smallest of all animals. We also assembled another non-eriophyid mite genome from accidental DNA bycatch (69.4Mb). We placed this new genomic resource in a phylogenetic context to reveal that mites have highly dynamic genome evolution, with a significant trend in genome downsizing in the eriophyoids. Our results suggest that this streamlining is associated with non-genic elements such as the suppression or excision of retrotransposons and purging of introns. As new sequencing techniques become available, novel genomic resources for tiny organisms such as F. perrepae will be more readily accessible, facilitating both fundamental genome evolutionary biology and applied sciences such as biological control programs which use eriophyoid mites for the management of invasive species.

evolutionary biology↗

bioRxiv2025

The genomics of convergent adaptation to intertidal gravel beaches in Mediterranean clingfishes

IntroductionUnderstanding the genetic basis of widespread phenotypic convergence, particularly for complex morphological traits, remains a major challenge in evolutionary biology. The Mediterranean gravel beach clingfishes of the genus Gouania provide an excellent system to study this phenomenon. Within this genus, two distinct morphotypes, "slender" and "stout", have repeatedly evolved, adapting to different microhabitats. These morphotypes differ in multiple complex traits, including body elongation, head compression, vertebral number, eye size, and the structure of the adhesive disc. Materials and MethodsIn a first step, to scrutinize phylogenetic convergence, we combined 3D morphometrics of the pelvic girdle and skull, with molecular species delimitation based on >660 DNA barcodes, and a phylogenomic framework based on more than 3,400 single-copy orthologs. Secondly, by employing whole-genome resequencing and a novel "convergence score" statistic, we examined genomic convergence across multiple levels: nucleotides, sequences, genes, and functional pathways. Results and DiscussionWhile we found no evidence of large-scale genomic or protein-level convergence, we identified promising candidate regions at the level of single variants, genes, and biological pathways. Notably, a longer shared (but interrupted) haplotype around the morphogene adam12 was associated with convergent traits. The lack of simple genomic patterns may reflect the radiations age and the complex genetic basis of the underlying morphological traits (e.g., eye-size, neurocranium shape). Altogether, our findings highlight the importance of assessing genomic convergence at multiple molecular levels to uncover diagnostic signals across varying evolutionary processes and timescales. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/675783v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@58265eorg.highwire.dtl.DTLVardef@13f1deaorg.highwire.dtl.DTLVardef@c51d79org.highwire.dtl.DTLVardef@112217d_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2020

Genetic similarity and facial cues for kin recognition in humans

Kin recognition is essential to the evolution of human cooperation, social organization, and altruistic behavior. However, the genetic underpinnings of kin recognition have been largely understudied. Facial resemblance is an important relatedness cue for humans and more closely related individuals are generally thought to share greater facial similarity. To evaluate the relationship between perceived self-resemblance and genetic similarity among biologically related and unrelated females, we administered facial self-recognition surveys to twenty-three sets of related females and genotyped three different genetic systems, human leukocyte antigens (HLA), neutral nuclear microsatellites and mitochondrial haplogroups, for each individual. Using these data, we examined the relationship between visual kin recognition and genetic similarity. We found that pairs of individuals identified as visually more similar had greater HLA allelic sharing when compared to less facially similar participants. We did not find the same relationship for microsatellite and mitochondrial similarity, suggesting that HLA allelic similarity increases the probability of perceived self-resemblance in humans while other genetic markers do not. Our results demonstrate that some genetic markers, such as HLA-DRB, may have significant influence on phenotype and that large scale surveys of HLA and facial feature morphology will yield valuable insight into the evolutionary biology of genotype-phenotype relationships and kin recognition.

evolutionary biology↗

bioRxiv2023

Bijections between the multifurcating unlabeled rooted trees and the positive integers

AO_SCPLOWBSTRACTC_SCPLOWColijn and Plazzotta (Systematic Biology 67:113-126, 2018) described a bijective scheme for associating the unlabeled bifurcating rooted trees with the positive integers. In mathematical and biological applications of unlabeled rooted trees, however, nodes of rooted trees are sometimes multifurcating rather than bifurcating. Building on the bijection between the unlabeled bifurcating rooted trees and the positive integers, we describe bijective schemes for associating the unlabeled multifurcating rooted trees with the positive integers. We devise bijections with the positive integers for a set of trees in which each non-leaf node has exactly k child nodes, and for a set of trees in which each non-leaf node has at most k child nodes. The calculations make use of Macaulays binomial expansion formula. The generalization to multifurcating trees can assist with the use of unlabeled trees for applications in evolutionary biology, such as the measurement of phylogenetic patterns of genetic lineages in pathogens. Mathematics subject classification (2020)05C05, 05C30, 92D15

evolutionary biology↗

bioRxiv2016

Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multi-locus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing 9 of the 11 major lineages and 10 non-yeast fungal outgroups to generate a 1,233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the 9 major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, 8 of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and of Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

Evolutionary Biology↗

bioRxiv2017

Selection On Morphological Traits And Fluctuating Asymmetry By A Fungal Parasite In The Yellow Dung Fly

A Preprint reviewed and recommended by Peer Community Evolutionary Biology: http://dx.doi.org/10.24072/pci.evolbiol.100027\n\nEvidence for selective disadvantages of large body size remains scarce in general. Previous phenomenological studies of the yellow dung fly Scathophaga stercoraria have demonstrated strong positive sexual and fecundity selection on male and female size. Nevertheless, the body size of flies from a Swiss study population has declined by almost 10% from 1993 to 2009. Given substantial heritability of body size, this negative evolutionary response of an evidently positively selected trait suggests important selective factors being missed (e.g. size-selective predation or parasitism). A periodic epidemic outbreak of the fungus Entomophthora scatophagae allowedassessment of selection exerted by this parasite fatal to adult flies. Fungal infection varied over the season from ca. 50% in the cooler and more humid spring and autumn to almost 0% in summer. The probability of dying from fungal infection increased with adult body size. All infected females died before laying eggs, so there was no fungus impact on female fecundity beyond its impact on mortality. Large males showed the typical mating advantage in the field, but this pattern of positive sexual selection was nullified by fungal infection. Mean fluctuating asymmetry of paired appendages (legs, wings) did not affect the viability, fecundity or mating success of yellow dung flies in the field. This study demonstrates rare parasite-mediated disadvantages of large adult body size in the field. Reduced ability to combat parasites such as Entomophthora may be an immunity cost of large size in dung flies, although the hypothesized trade-off between fluctuating asymmetry, a presumed indicator of developmental instability and environmental stress, and immunocompetence was not found here.

evolutionary biology↗

bioRxiv2019

Topological constraints in early multicellularity favor reproductive division of labor

Reproductive division of labor (e.g., germ-soma specialization) is a hallmark of the evolution of multicellularity, signifying the emergence of a new type of individual and facilitating the evolution of increased organismal complexity. A large body of work from evolutionary biology, economics, and ecology has shown that specialization is beneficial when further division of labor produces an accelerating increase in absolute productivity (i.e., productivity is a convex function of specialization). Here we show that reproductive specialization is qualitatively different from classical models of resource sharing, and can evolve even when the benefits of specialization are saturating (i.e., productivity is a concave function of specialization). Through analytical theory and evolutionary individual based simulations, our work demonstrates that reproductive specialization is strongly favored in sparse networks of cellular interactions, such as trees and filaments, that reflect the morphology of early, simple multicellular organisms, highlighting the importance of restricted social interactions in the evolution of reproductive specialization. More broadly, we find that specialization is strongly favored, despite saturating returns on investment, in a wide range of scenarios in which sharing is asymmetric.

evolutionary biology↗

bioRxiv2023

Constraint and innovation in color evolution among species and among plumage patches in five avian radiations

Understanding the causes and limits of phenotypic diversification remains a key challenge in evolutionary biology. Color patterns are some of the most diverse phenotypes in nature. In birds, recent work within families has suggested that plumage complexity might be a key innovation driving color diversity. Whether these patterns hold at larger taxonomic scales remains unknown. Here, we assemble a large database of UV-Vis spectral data across five diverse clades of birds (45791 spectra, 1135 species). Using multivariate phylogenetic comparative methods, we compare evolutionary rates and color space occupancy (i.e., quantification of observed colors) among these clades. Novel color-producing mechanisms have enabled clades to occupy new regions of color space, but using more coloration mechanisms did not result in overall more color space occupancy. Instead, the use of more color-producing mechanisms resulted in faster rates of color evolution and less integrated color among plumage regions. Flexible Bayesian modeling further allowed us to assess the relationship between interpatch and interspecific directions of color variation. We find that interpatch variation generally diverges from interspecies cladewise trends in males but not females, suggesting developmental or selective constraints operating in females across evolutionary scales. By comparing rates among clades and assessing both interpatch and interspecies color variation, we reveal how innovations and constraints operate across evolutionary and developmental scales.

evolutionary biology↗