Macroevolutionary convergence connects morphological form to ecological function in birds

Urbanization reduces diversity, simplifies community and filter bird species based on their functional traits in a tropical city

Understanding how organisms are coping with major changes imposed by urban intensification is a complex task. In fact, our understanding of the impacts of urbanization on biodiversity is scarce in the global south compared to the north. In this study, we evaluated how bird communities are affected by impact of urban intensification in a tropical city. Thus, we assessed whether increased urban intensification 1) jeopardizes bird diversity (taking into account taxonomic-TD, phylogenetic-PD, and functional-FD dimensions), 2) drives changes in bird community composition and enables the detection of indicator species of such impact, and 3) leads to changes in bird functional traits linked to reproduction, resource acquisition, and survival. We found that urban intensification has a direct impact on the bird community, reducing all three types of diversity. Communities in areas of greater urban intensity are represented by fewer species, and these species are PD and FD less distinct. In addition, we detected at least ten species of areas of lower urban intensity that proved to be more sensitive to urban intensification. With regard to bird traits, we found no significant responses from reproductive, habitat use and feeding variables. Body weight and tail length were the only variables with significant results, with higher urbanization intensity areas selecting for species with lower weights and longer tails. Given the global biodiversity loss we are observing, this information can guide urban managers and planners in designing urban landscapes to maintain biodiversity in cities.

Macroevolution of the plant-hummingbird pollination system

Plant-hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant-hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre-dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build-up of both diversities coinciding temporally, and hence suggesting co-diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species-level interaction data in macroevolutionary studies.

Synthetic analysis of trophic diversity and evolution in Enantiornithes with new insights from Bohaiornithidae

Enantiornithines were the dominant birds of the Mesozoic, but understanding of their diet is still tenuous. We introduce new data on the enantiornithine family Bohaiornithidae, famous for their large size and powerfully built teeth and claws. In tandem with previously published data, we comment on the breadth of enantiornithine ecology and potential patterns in which it evolved. Body mass, jaw mechanical advantage, finite element analysis of the jaw, and traditional morphometrics of the claws and skull are compared between bohaiornithids and living birds. We find bohaiornithids to be more ecologically diverse than any other enantiornithine family: Bohaiornis and Parabohaiornis are similar to living plant-eating birds; Longusunguis resembles raptorial carnivores; Zhouornis is similar to both fruit-eating birds and generalist feeders; and Shenqiornis and Sulcavis plausibly ate fish, plants, or a mix of both. We predict the ancestral enantiornithine bird to have been a generalist which ate a wide variety of foods. However, more quantitative data from across the enantiornithine tree is needed to refine this prediction. By the Early Cretaceous, enantiornithine birds had diversified into a variety of ecological niches like crown birds after the K-Pg extinction, adding to the evidence that traits unique to crown birds cannot completely explain their ecological success.

Impacts of coprophagic foraging behaviour on the avian gut microbiome

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.

Recent genetic, phenetic and ecological divergence across the Mesoamerican highlands: a study case with Diglossa baritula (Aves: Thraupidae)

The topographical, geological, climatic and biodiversity complexity of Mesoamerica has made it a primary research focus. The Mesoamerican highlands is a region with particularly high species richness and within-species variation. The Cinnamon-bellied Flowerpiercer, Diglossa baritula (Wagler, 1832), is a species endemic to the Mesoamerican highlands, with three allopatric subspecies currently recognized. To characterize divergence within this species, we integrated genomics, morphology, coloration and ecological niche modeling approaches, obtained from sampling individuals across the entire geographic distribution of the species. Our results revealed a clear genomic divergence between the populations to the east versus the west of the Isthmus of Tehuantepec. In contrast to the genomic results, morphology and coloration analyses showed intermediate levels of differentiation, indicating that population groups within D. baritula have probably been under similar selective pressures. Our morphology results indicated that the only sexually dimorphic morphological variable is the wing chord, with males having a longer wing chord than females. Finally, ecological data indicated that there are differences in ecological niche within D. baritula. Our data suggest that D. baritula could contain two or more incipient species at the intermediate phase of the speciation continuum. These results highlight the importance of the geographical barrier of the Isthmus of Tehuantepec and Pleistocene climatic events in driving isolation and population divergence in D. baritula. The present investigation illustrates the speciation potential of the D. baritula complex and the capacity of Mesoamerican highlands to create cryptic biodiversity and endemism.

Loss of species and functions in a deforested megadiverse tropical forest

Tropical species richness is threatened by habitat degradation associated with land-use conversion, yet the consequences for functional diversity remain little understood. Progress has been hindered by difficulties in obtaining comprehensive species-level trait information to characterize entire assemblages and insufficient appreciation that increasing land-cover heterogeneity potentially compensates for species loss. We examined the impacts of tropical deforestation associated with land-use heterogeneity on bird species richness, functional redundancy, functional diversity, and associated components (i.e., alpha diversity, species dissimilarity, and interaction strength of the relationship between abundance and functional dissimilarity). We analyzed over 200 georeferenced bird assemblages in the Atlantic Forest of Brazil. We characterized the functional role of the species of each assemblage and modeled biodiversity metrics as a function of forest cover and land-cover heterogeneity. Replacement of native Atlantic Forest with a mosaic of land uses (e.g., agriculture, pastures, and urbanization) reduced bird species richness in a nonrandom way. Core forest species, or species considered sensitive to edges, tended to be absent in communities in heterogenous environments. Overall, functional diversity and functional redundancy of bird species were not affected by forest loss. However, birds in highly heterogenous habitats were functionally distinct from birds in forest, suggesting a shift in community composition toward mosaic-exclusive species led by land-cover heterogeneity. Threatened species of the Atlantic Forest did not seem to tolerate degraded and heterogeneous environments; they remained primarily in areas with large forest tracts. Our results shed light on the complex effects of native forest transformation to mosaics of anthropogenic landscapes and emphasize the importance of considering the effects of deforestation and land-use heterogeneity when assessing deforestation effects on Neotropical biodiversity.

Land-use change interacts with island biogeography to alter bird community assembly

Anthropogenic activities have reshaped biodiversity on islands worldwide. However, it remains unclear how island attributes and land-use change interactively shape multiple facets of island biodiversity through community assembly processes. To answer this, we conducted bird surveys in various land-use types (mainly forest and farmland) using transects on 34 oceanic land-bridge islands in the largest archipelago of China. We found that bird species richness increased with island area and decreased with isolation, regardless of the intensity of land-use change. However, forest-dominated habitats exhibited lower richness than farmland-dominated habitats. Island bird assemblages generally comprised species that share more similar traits or evolutionary histories (i.e. functional and/or phylogenetic clustering) than expected if assemblages were randomly assembled. Contrary to our expectations, we observed that bird assemblages in forest-dominated habitats were more clustered on large and close islands, whereas assemblages in farmland-dominated habitats were more clustered on small islands. These contrasting results indicate that land-use change interacts with island biogeography to alter the community assembly of birds on inhabited islands. Our findings emphasize the importance of incorporating human-modified habitats when examining the community assembly of island biota, and further suggest that agricultural landscapes on large islands may play essential roles in protecting countryside island biodiversity.

A slow-fast trait continuum at the whole community level in relation to land-use intensification

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.

Limited ecological opportunity influences the tempo of morphological evolution in birds

According to classic models of lineage diversification and adaptive radiation, phenotypic evolution should accelerate in the context of ecological opportunity and slow down when niches become saturated.1,2 However, only weak support for these ideas has been found in nature, perhaps because most analyses make the biologically unrealistic assumption that clade members contribute equally to reducing ecological opportunity, even when they occur in different continents or specialize on different habitats and diets. To view this problem through a different lens, we adapted a new phylogenetic modeling approach that accounts for the fact that competition for ecological opportunity only occurs between species that coexist and share similar habitats and diets. Applying this method to trait data for nearly all extant species of landbirds,3 we find a widespread signature of decelerating trait evolution in lineages adapted to similar habitats or diets. The strength of this pattern was consistent across latitudes when comparing tropical and temperate assemblages. Our results provide little support for the idea that increased diversity and tighter packing of niches accentuates evolutionary slowdowns in the tropics and instead suggest that limited ecological opportunity can be an important factor determining the rate of morphological diversification at a global scale.

Geographic variations in eco-evolutionary factors governing urban birds: The case of university campuses in China

Urbanization alters natural habitats, restructures biotic communities and serves as a filter for selecting species from regional species pools. However, empirical evidence of the specific traits that allow species to persist in urban areas yields mixed results. More importantly, it remains unclear which traits are widespread for species utilizing urban spaces (urban utilizers) and which are environment-dependent traits. Using 745 bird species from 287 university/institute campuses in 74 cities and their species pools across China, we tested whether species that occur in urban areas are correlated with regards to their biological (body mass, beak shape, flight capacity and clutch size), ecological (diet diversity, niche width and habitat breadth), behavioural (foraging innovation) and evolutionary (diversification rate) attributes. We used Bayesian phylogenetic generalized linear mixed models to disentangle the relative roles of these predictors further, and to determine the extent to which the effects of these predictors varied among different cities. We found that urban birds were more phylogenetically clustered than expected by chance, and were generally characterized by a larger habitat breadth, faster diversification rate, more behavioural innovation and smaller body size. Notably, the relative effects of the attributes in explaining urban bird communities varied with city temperature and elevation, indicating that the filters used to determine urban species were environment dependent. We conclude that, while urban birds are typically small-sized, generalists, innovative and rapidly diversifying, the key traits that allow them to thrive vary spatially, depending on the climatic and topographic conditions of the city. These findings emphasize the importance of studying species communities within specific cities to better understand the contextual dependencies of key traits that are filtered by urban environments.

Contrasting impacts of non-native and threatened species on morphological, life history, and phylogenetic diversity in bird assemblages

Human activities have altered the species composition of assemblages through introductions and extinctions, but it remains unclear how those changes can affect the different facets of biodiversity. Here we assessed the impact of changes in species composition on taxonomic, functional, and phylogenetic diversity across 281 bird assemblages worldwide. To provide a more nuanced understanding of functional diversity, we distinguished morphological from life-history traits. We showed that shifts in species composition could trigger a global decline in avian biodiversity due to the high number of potential extinctions. Moreover, these extinctions were not random but unique in terms of function and phylogeny at the regional level. Our findings demonstrated that non-native species cannot compensate for these losses, as they are both morphologically and phylogenetically close to the native fauna. In the context of the ongoing biodiversity crisis, such alterations in the functional and phylogenetic structure of bird assemblages could heighten ecosystem vulnerability.

Assessing the predictive value of morphological traits on primary lifestyle of birds through the extreme gradient boosting algorithm

The relationship between morphological traits and ecological performance in birds is an important area of research, as it can help us to understand how birds are able to adapt and how they are affected by changes in their environment. Many studies have investigated the relationship between morphological traits and certain aspects of the performance and ecological niche of these animals. However, the relationship between morphological traits and the primary lifestyle of birds has not previously been explored. This paper aims to evaluate the predictive potential of morphological data to determine the primary lifestyle of birds through a tree-based machine learning algorithm. By doing this, it is also possible to evaluate these artificial categories that we used to split up birds and know whether they are suitable for dividing them in function of shared morphological characteristics or need a redefinition under more discriminant criteria. Supplementary dataset 1 of the AVONET project was used, which comprises the 11 morphological predictors used in this work and the classification according to the primary lifestyle for more than 95% of the existing bird species. For all morphological traits used, statistically significant univariate differences were found between primary lifestyles. The three fitted machine learning models showed high accuracy, in all cases above 78% and superior to the ones achieved through traditional approaches used as contrasts. The results obtained provide evidence that primary lifestyle can be predicted in birds based on morphological traits, as well as more insights about the relevance of functional traits for ecological modeling. This is another step forward in our mechanistic understanding of bird ecology, while exploring how birds have adapted to their environments and how they interact with their surroundings.

Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change

Determining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.

Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs

Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.

Global patterns of plumage color evolution in island-living passeriform birds

Island environments have the potential to change evolutionary trajectories of morphological traits in species relative to their mainland counterparts due to habitat and resource differences, or by reductions in the intensity of social or sexual selection. Latitude, island size, and isolation may further influence trait evolution through biases in colonization rates. We used a global dataset of passerine plumage color as a model group to identify selective pressures driving morphological evolution of island animals using phylogenetically-controlled analyses. We calculated chromaticity values from red and blue scores extracted from images of the majority of Passeriformes and tested these against the factors hypothesized to influence color evolution. In contrast to predictions based on sexual and social selection theory, we found consistent changes in island female color (lower red and higher blue chromaticity), but no change in males. Instead, island size and distance from mainland and other islands influenced color in both sexes, reinforcing the importance of island physiognomy in shaping evolutionary processes. Interactions between ecological factors and latitude also consistently influenced color for both sexes, supporting a latitudinal gradient hypothesis. Finally, patterns of color evolution varied among families, indicating taxon-specific microevolutionary processes in driving color evolution. Our results show island residency influences color evolution differently between sexes, but the patterns in both sexes are tempered by ecological, island characteristics, and phylogenetic effects that further vary in their importance among families. The key role of environmental factors in shaping bird plumage on islands further suggests a reduced importance of sexual and social factors in driving color evolution.

Food transport in Reptilia: a comparative viewpoint

Reptilia exploit a large diversity of food resources from plant materials to living mobile prey. They are among the first tetrapods that needed to drink to maintain their water homeostasis. Here were compare the feeding and drinking mechanisms in Reptilia through an empirical approach based on the available data to open perspectives in our understanding of the evolution of the various mechanisms determined in these Tetrapoda for exploiting solid and liquid food resources. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

Trait-Based Paleontological Niche Prediction Recovers Extinct Ecological Breadth of the Earliest Specialized Ant Predators

AbstractPaleoecological estimation is fundamental to the reconstruction of evolutionary and environmental histories. The ant fossil record preserves a range of species in three-dimensional fidelity and chronicles faunal turnover across the Cretaceous and Cenozoic; taxonomically rich and ecologically diverse, ants are an exemplar system to test new methods of paleoecological estimation in evaluating hypotheses. We apply a broad extant ecomorphological dataset to evaluate random forest machine learning classification in predicting the total ecological breadth of extinct and enigmatic hell ants. In contrast to previous hypotheses of extinction-prone arboreality, we find that hell ants were primarily leaf litter or ground-nesting and foraging predators, and by comparing ecospace occupations of hell ants and their extant analogs, we recover a signature of ecomorphological turnover across temporally and phylogenetically distinct lineages on opposing sides of the Cretaceous-Paleogene boundary. This paleoecological predictive framework is applicable across lineages and may provide new avenues for testing hypotheses over deep time.

Classification and distribution of functional groups of birds and mammals in Mexico

There has been a recent exponential growth in the study of functional trait ecology. Nonetheless, the study of functional traits and functional groups has been limited for terrestrial vertebrates. We conducted a classification update of functional groups (FG) of birds and mammals in Mexico, and determined the distribution patterns of FG species richness in different ecosystems nationwide. We selected six functional traits (feeding habit, locomotion, feeding substrate and technique, activity period, seasonality, and body size) obtained for 987 and 496 species of birds and mammals, respectively. A cophenetic correlation analyses resulted in values of 0.82 for the bird species dendrogram, and 0.79 for the mammal species dendrogram showing that the structures adequately reflected the similarity between observations. We obtained 52 FG for birds, assembled into 9 broader groups based on their feeding habits (16 invertivores, 6 carnivores: 5 herbivores, 9 aquatic vertivore/invertivore, 5 granivores, 1 scavenger, 3 nectarivores, 4 frugivores, and 3 omnivores). We obtained 35 FG for mammals, assembled into 9 broader groups based on their feeding habits (4 granivores, 10 herbivores, 1 nectarivore, 4 frugivores, 8 invertivores, 3 omnivores, 2 aquatic vertivore/invertivore, 1 hematophagous, and 2 carnivores). Overall, the distribution of FG species richness for birds and mammals gradually increased from the Nearctic to the Neotropical region, following a typical latitudinal species richness pattern. Few FG of migratory birds, and FG of granivore and herbivore mammals showed more species in the Nearctic and in the transitional regions. Our study provides a baseline for identifying ecological functions of species of birds and mammals in different ecosystems in Mexico, and contributes to understand the relationship between species diversity, community structure and ecosystem functioning. Identifying spatial patterns of functional trait diversity is important as biodiversity loss has a negative impact on ecosystem functioning and provision of environmental services.

What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate

AbstractIn January 2018, Sharon Strauss, then president of the American Society of Naturalists, organized a debate on the following topic: does evolutionary history inform the current functioning of ecological communities? The debaters-Ives, Lau, Mayfield, and Tobias-presented pro and con arguments, caricatured in standard debating format. Numerous examples show that both recent microevolutionary and longer-term macroevolutionary history are important to the ecological functioning of communities. On the other hand, many other examples illustrate that the evolutionary history of communities or community members does not influence ecological function, or at least not very much. This article aims to provide a provocative discussion of the consistent and conflicting patterns that emerge in the study of contemporary and historical evolutionary influences on community function, as well as to identify questions for further study. It is intended as a thought-provoking exercise to explore this complex field, specifically addressing (1) key assumptions and how they can lead us astray and (2) issues that need additional study. The debaters all agree that evolutionary history can inform us about at least some aspects of community function. The underlying question at the root of the debate, however, is how the fields of ecology and evolution can most profitably collaborate to provide a deeper and broader understanding of ecological communities.

Innovation and elaboration on the avian tree of life

Widely documented, megaevolutionary jumps in phenotypic diversity continue to perplex researchers because it remains unclear whether these marked changes can emerge from microevolutionary processes. Here, we tackle this question using new approaches for modeling multivariate traits to evaluate the magnitude and distribution of elaboration and innovation in the evolution of bird beaks. We find that elaboration, evolution along the major axis of phenotypic change, is common at both macro- and megaevolutionary scales, whereas innovation, evolution away from the major axis of phenotypic change, is more prominent at megaevolutionary scales. The major axis of phenotypic change among species beak shapes at megaevolutionary scales is an emergent property of innovation across clades. Our analyses suggest that the reorientation of phenotypes via innovation is a ubiquitous route for divergence that can arise through gradual change alone, opening up further avenues for evolution to explore.

Mercury in Neotropical birds: a synthesis and prospectus on 13 years of exposure data

Environmental mercury (Hg) contamination of the global tropics outpaces our understanding of its consequences for biodiversity. Knowledge gaps of pollution exposure could obscure conservation threats in the Neotropics: a region that supports over half of the world's species, but faces ongoing land-use change and Hg emission via artisanal and small-scale gold mining (ASGM). Due to their global distribution and sensitivity to pollution, birds provide a valuable opportunity as bioindicators to assess how accelerating Hg emissions impact an ecosystem's ability to support biodiversity, and ultimately, global health. We present the largest database on Neotropical bird Hg concentrations (n = 2316) and establish exposure baselines for 322 bird species spanning nine countries across Central America, South America, and the West Indies. Patterns of avian Hg exposure in the Neotropics broadly align with those in temperate regions: consistent bioaccumulation across functional groups and high spatiotemporal variation. Bird species occupying higher trophic positions and aquatic habitats exhibited elevated Hg concentrations that have been previously associated with reductions in reproductive success. Notably, bird Hg concentrations were over four times higher at sites impacted by ASGM activities and differed by season for certain trophic niches. We developed this synthesis via a collaborative research network, the Tropical Research for Avian Conservation and Ecotoxicology (TRACE) Initiative, which exemplifies inclusive, equitable, and international data-sharing. While our findings signal an urgent need to assess sampling biases, mechanisms, and consequences of Hg exposure to tropical avian communities, the TRACE Initiative provides a meaningful framework to achieve such goals. Ultimately, our collective efforts support and inform local, scientific, and government entities, including Parties of the United Nations Minamata Convention on Mercury, as we continue working together to understand how Hg pollution impacts biodiversity conservation, ecosystem function, and public health in the tropics.

Beak morphometry and morphogenesis across avian radiations

Adaptive avian radiations associated with the diversification of bird beaks into a multitude of forms enabling different functions are exemplified by Darwin's finches and Hawaiian honeycreepers. To elucidate the nature of these radiations, we quantified beak shape and skull shape using a variety of geometric measures that allowed us to collapse the variability of beak shape into a minimal set of geometric parameters. Furthermore, we find that just two measures of beak shape-the ratio of the width to length and the normalized sharpening rate (increase in the transverse beak curvature near the tip relative to that at the base of the beak)-are strongly correlated with diet. Finally, by considering how transverse sections to the beak centreline evolve with distance from the tip, we show that a simple geometry-driven growth law termed 'modified mean curvature flow' captures the beak shapes of Darwin's finches and Hawaiian honeycreepers. A surprising consequence of the simple growth law is that beak shapes that are not allowed based on the developmental programme of the beak are also not observed in nature, suggesting a link between evolutionary morphology and development in terms of growth-driven developmental constraints.

Bird clades with less complex appendicular skeletons tend to have higher species richness

Species richness is strikingly uneven across taxonomic groups at all hierarchical levels, but the reasons for this heterogeneity are poorly understood. It is well established that morphological diversity (disparity) is decoupled from taxonomic diversity, both between clades and across geological time. Morphological complexity has been much less studied, but there is theory linking complexity with differential diversity across groups. Here we devise an index of complexity from the differentiation of the fore and hind limb pairs for a sample of 983 species of extant birds. We test the null hypothesis that this index of morphological complexity is uncorrelated with clade diversity, revealing a significant and negative correlation between the species richness of clades and the mean morphological complexity of those clades. Further, we find that more complex clades tend to occupy a smaller number of dietary and habitat niches, and that this proxy for greater ecological specialisation correlates with lower species richness. Greater morphological complexity in the appendicular skeleton therefore appears to hinder the generation and maintenance of species diversity. This may result from entrenchment into morphologies and ecologies that are less capable of yielding further diversity.

Binocular vision and foraging in ducks, geese and swans (Anatidae)

Wide variation in visual field configuration across avian species is hypothesized to be driven primarily by foraging ecology and predator detection. While some studies of selected taxa have identified relationships between foraging ecology and binocular field characteristics in particular species, few have accounted for the relevance of shared ancestry. We conducted a large-scale, comparative analysis across 39 Anatidae species to investigate the relationship between the foraging ecology traits of diet or behaviour and binocular field parameters, while controlling for phylogeny. We used phylogenetic models to examine correlations between traits and binocular field characteristics, using unidimensional and morphometric approaches. We found that foraging behaviour influenced three parameters of binocular field size: maximum binocular field width, vertical binocular field extent, and angular separation between the eye-bill projection and the direction of maximum binocular field width. Foraging behaviour and body mass each influenced two descriptors of binocular field shape. Phylogenetic relatedness had minimal influence on binocular field size and shape, apart from vertical binocular field extent. Binocular field differences are associated with specific foraging behaviours, as related to the perceptual challenges of obtaining different food items from aquatic and terrestrial environments.

Feedback loops between 3D vegetation structure and ecological functions of animals

Ecosystems function in a series of feedback loops that can change or maintain vegetation structure. Vegetation structure influences the ecological niche space available to animals, shaping many aspects of behaviour and reproduction. In turn, animals perform ecological functions that shape vegetation structure. However, most studies concerning three-dimensional vegetation structure and animal ecology consider only a single direction of this relationship. Here, we review these separate lines of research and integrate them into a unified concept that describes a feedback mechanism. We also show how remote sensing and animal tracking technologies are now available at the global scale to describe feedback loops and their consequences for ecosystem functioning. An improved understanding of how animals interact with vegetation structure in feedback loops is needed to conserve ecosystems that face major disruptions in response to climate and land-use change.

Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)

The upper and lower jaws of some wrasses (Eupercaria: Labridae) possess teeth that have been coalesced into a strong durable beak that they use to graze on hard coral skeletons, hard-shelled prey, and algae, allowing many of these species to function as important ecosystem engineers in their respective marine habitats. While the ecological impact of the beak is well understood, questions remain about its evolutionary history and the effects of this innovation on the downstream patterns of morphological evolution. Here we analyze 3D cranial shape data in a phylogenetic comparative framework and use paleoclimate modeling to reconstruct the evolution of the labrid beak across 205 species. We find that wrasses evolved beaks three times independently, once within odacines and twice within parrotfishes in the Pacific and Atlantic Oceans. We find an increase in the rate of shape evolution in the Scarus+Chlorurus+Hipposcarus (SCH) clade of parrotfishes likely driven by the evolution of the intramandibular joint. Paleoclimate modeling shows that the SCH clade of parrotfishes rapidly morphologically diversified during the middle Miocene. We hypothesize that possession of a beak in the SCH clade coupled with favorable environmental conditions allowed these species to rapidly morphologically diversify.

Online repositories of photographs and videos provide insights into the evolution of skilled hindlimb movements in birds

The ability to manipulate objects with limbs has evolved repeatedly among land tetrapods. Several selective forces have been proposed to explain the emergence of forelimb manipulation, however, work has been largely restricted to mammals, which prevents the testing of evolutionary hypotheses in a comprehensive evolutionary framework. In birds, forelimbs have gained the exclusive function of flight, with grasping transferred predominantly to the beak. In some birds, the feet are also used in manipulative tasks and appear to share some features with manual grasping and prehension in mammals, but this has not been systematically investigated. Here we use large online repositories of photographs and videos to quantify foot manipulative skills across a large sample of bird species (>1000 species). Our results show that a complex interaction between niche, diet and phylogeny drive the evolution of manipulative skills with the feet in birds. Furthermore, we provide strong support for the proposition that an arboreal niche is a key element in the evolution of manipulation in land vertebrates. Our systematic comparison of foot use in birds provides a solid base for understanding morphological and neural adaptations for foot use in birds, and for studying the convergent evolution of manipulative skills in birds and mammals.

Co-migration fidelity at a stopover site increases over time in African-European migratory landbirds

Migratory species are changing their timing of departure from wintering areas and arrival to breeding sites (i.e. migration phenology) in response to climate change to exploit maximum food availability at higher latitudes and improve their fitness. Despite the impact of changing migration phenology at population and community level, the extent to which individual and species-specific response affects associations among co-migrating species has been seldom explored. By applying temporal co-occurrence network models on 15 years of standardized bird ringing data at a spring stopover site, we show that African-European migratory landbirds tend to migrate in well-defined groups of species with high temporal overlap. Such 'co-migration fidelity' significantly increased over the years and was higher in long-distance (trans-Saharan) than in short-distance (North African) migrants. Our findings suggest non-random patterns of associations in co-migrating species, possibly related to the existence of regulatory mechanisms associated with changing climate conditions and different uses of stopover sites, ultimately influencing the global economy of migration of landbirds in the Palearctic-African migration system.

Low morphological disparity and decelerated rate of limb size evolution close to the origin of birds

The origin of birds from theropod dinosaurs involves many changes in musculoskeletal anatomy and epidermal structures, including multiple instances of convergence and homology-related traits that contribute to the refinement of flight capability. Changes in limb sizes and proportions are important for locomotion (for example, the forelimb for bird flight); thus, understanding these patterns is central to investigating the transition from terrestrial to volant theropods. Here we analyse the patterns of morphological disparity and the evolutionary rate of appendicular limbs along avialan stem lineages using phylogenetic comparative approaches. Contrary to the traditional wisdom that an evolutionary innovation like flight would promote and accelerate evolvability, our results show a shift to low disparity and decelerated rate near the origin of avialans that is largely ascribed to the evolutionarily constrained forelimb. These results suggest that natural selection shaped patterns of limb evolution close to the origin of avialans in a way that may reflect the winged forelimb 'blueprint' associated with powered flight.

Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

Intrinsic and extrinsic drivers of shape variation in the albatross compound bill

Albatross are the largest seabirds on Earth and have a suite of adaptations for their pelagic lifestyle. Rather than having a bill made of a single piece of keratin, Procellariiformes have a compound rhamphotheca, made of several joined plates. Drivers of the shape of the albatross bill have not been explored. Here we use three-dimensional scans of 61 upper bills from 12 species of albatross to understand whether intrinsic (species assignment & size) or extrinsic (diet) factors predict bill shape. Diet is a significant predictor of bill shape with coarse dietary categories providing higher R2 values than dietary proportion data. We also find that of the intrinsic factors, species assignment accounts for ten times more of the variation than size (72% versus 6.8%) and that there is a common allometric vector of shape change between all species. When considering species averages in a phylogenetic framework, there are significant Blomberg's K results for both shape and size (K = 0.29 & 1.10) with the first axis of variation having a much higher K value (K = 1.9), reflecting the split in shape at the root of the tree. The influence of size on bill shape is limited, with species assignment and diet predicting far more of the variation. The results show that both intrinsic and extrinsic factors are needed to understand morphological evolution.

Complementarity in Allen's and Bergmann's rules among birds

Biologists have long noted that endotherms tend to have larger bodies (Bergmann's rule) and shorter appendages (Allen's rule) in colder environments. Nevertheless, many taxonomic groups appear not to conform to these 'rules', and general explanations for these frequent exceptions are currently lacking. Here we note that by combining complementary changes in body and extremity size, lineages could theoretically respond to thermal gradients with smaller changes in either trait than those predicted by either Bergmann's or Allen's rule alone. To test this idea, we leverage geographic, ecological, phylogenetic, and morphological data on 6,974 non-migratory terrestrial bird species, and show that stronger family-wide changes in bill size over thermal gradients are correlated with more muted changes in body size. Additionally, we show that most bird families exhibit weak but appropriately directed changes in both traits, supporting the notion of complementarity in Bergmann's and Allen's rules. Finally, we show that the few families that exhibit significant gradients in either bill or body size, tend to be more speciose, widely distributed, or ecologically constrained. Our findings validate Bergmann's and Allen's logic and remind us that body and bill size are simply convenient proxies for their true quantity of interest: the surface-to-volume ratio.

The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus

Long-distance migratory animals such as birds and bats have evolved to withstand selection imposed by pathogens across the globe, and pathogen richness is known to be particularly high in tropical regions. Immune genes, so-called Major Histocompatibility Complex (MHC) genes, are highly duplicated in songbirds compared to other vertebrates, and this high MHC diversity has been hypothesised to result in a unique adaptive immunity. To understand the rationale behind the evolution of the high MHC genetic diversity in songbirds, we determined the structural properties of an MHC class I protein, Acar3, from a long-distance migratory songbird, the great reed warbler Acrocephalus arundinaceus (in short: Acar). The structure of Acar3 was studied in complex with pathogen-derived antigens and shows an overall antigen presentation similar to human MHC class I. However, the peptides bound to Acar3 display an unusual conformation: Whereas the N-terminal ends of the peptides display enhanced flexibility, the conformation of their C-terminal halves is rather static. This uncommon peptide-binding mode in Acar3 is facilitated by a central Arg residue within the peptide-binding groove that fixes the backbone of the peptide at its central position, and potentially permits successful interactions between MHC class I and innate immune receptors. Our study highlights the importance of investigating the immune system of wild animals, such as birds and bats, to uncover unique immune mechanisms which may neither exist in humans nor in model organisms.

Climate-driven variation in dispersal ability predicts responses to forest fragmentation in birds

Species sensitivity to forest fragmentation varies latitudinally, peaking in the tropics. A prominent explanation for this pattern is that historical landscape disturbance at higher latitudes has removed fragmentation-sensitive species or promoted the evolution of more resilient survivors. However, it is unclear whether this so-called extinction filter is the dominant driver of geographic variation in fragmentation sensitivity, particularly because climatic factors may also cause latitudinal gradients in dispersal ability, a key trait mediating sensitivity to habitat fragmentation. Here we combine field survey data with a morphological proxy for avian dispersal ability (hand-wing index) to assess responses to forest fragmentation in 1,034 bird species worldwide. We find that fragmentation sensitivity is strongly predicted by dispersal limitation and that other factors-latitude, body mass and historical disturbance events-have relatively limited explanatory power after accounting for species differences in dispersal. We also show that variation in dispersal ability is only weakly predicted by historical disturbance and more strongly associated with intra-annual temperature fluctuations (seasonality). Our results suggest that climatic factors play a dominant role in driving global variation in the impacts of forest fragmentation, emphasizing the need for more nuanced environmental policies that take into account local context and associated species traits.

Bridging Performance and Adaptive Landscapes to Understand Long-Term Functional Evolution

AbstractUnderstanding functional adaptation demands an integrative framework that captures the complex interactions between form, function, ecology, and evolutionary processes. In this review, we discuss how to integrate the following two distinct approaches to better understand functional evolution: (1) the adaptive landscape approach (ALA), aimed at finding adaptive peaks for different ecologies, and (2) the performance landscape approach (PLA), aimed at finding performance peaks for different ecologies. We focus on the Ornstein-Uhlenbeck process as the evolutionary model for the ALA and on biomechanical modeling to estimate performance for the PLA. Whereas both the ALA and the PLA have each given insight into functional adaptation, separately they cannot address how much performance contributes to fitness or whether evolutionary constraints have played a role in form-function evolution. We show that merging these approaches leads to a deeper understanding of these issues. By comparing the locations of performance and adaptive peaks, we can infer how much performance contributes to fitness in species' current environments. By testing for the relevance of history on phenotypic variation, we can infer the influence of past selection and constraints on functional adaptation. We apply this merged framework in a case study of turtle shell evolution and explain how to interpret different possible outcomes. Even though such outcomes can be quite complex, they represent the multifaceted relations among function, fitness, and constraints.

Ecological and life-history drivers of avian skull evolution

One of the most famous examples of adaptive radiation is that of the Galápagos finches, where skull morphology, particularly the beak, varies with feeding ecology. Yet increasingly studies are questioning the strength of this correlation between feeding ecology and morphology in relation to the entire neornithine radiation, suggesting that other factors also significantly affect skull evolution. Here, we broaden this debate to assess the influence of a range of ecological and life-history factors, specifically habitat density, migration, and developmental mode, in shaping avian skull evolution. Using 3D geometric morphometric data to robustly quantify skull shape for 354 extant species spanning avian diversity, we fitted flexible phylogenetic regressions and estimated evolutionary rates for each of these factors across the full data set. The results support a highly significant relationship between skull shape and both habitat density and migration, but not developmental mode. We further found heterogenous rates of evolution between different character states within habitat density, migration, and developmental mode, with rapid skull evolution in species that occupy dense habitats, are migratory, or are precocial. These patterns demonstrate that diverse factors affect the tempo and mode of avian phenotypic evolution and that skull evolution in birds is not simply a reflection of feeding ecology.

Biomechanics illuminates form-function relationships in bird bills

The field of comparative biomechanics examines how form, mechanical properties and environmental interactions shape the function of biological structures. Biomechanics has advanced by leaps and bounds as rapid technological progress opens up new research horizons. In this Review, I describe how our understanding of the avian bill, a morphologically diverse multifunctional appendage, has been transformed by employing a biomechanical perspective. Across functions from feeding to excavating hollows in trees and as a vocal apparatus, the study of the bill spans both solid and fluid biomechanics, rendering it useful to understand general principles across disciplines. The different shapes of the bill across bird species result in functional and mechanical trade-offs, thus representing a microcosm of many broader form-function questions. Using examples from diverse studies, I discuss how research into bird bills has been shaped over recent decades, and its influence on our understanding of avian ecology and evolution. Next, I examine how bill material properties and geometry influence performance in dietary and non-dietary contexts, simultaneously imposing trade-offs on other functions. Following an examination of the interactions of bills with fluids and their role as part of the vocal apparatus, I end with a discussion of the sensory biomechanics of the bill, focusing specifically on the bill-tip mechanosensory organ. With these case studies, I highlight how this burgeoning and consequential field represents a roadmap for our understanding of the function and evolution of biological structures.

Testing the predictive value of functional traits in diverse ant communities

Associating morphological features with ecological traits is essential for understanding the connection between organisms and their roles in the environment. If applied successfully, functional trait approaches link form and function in an organism. However, functional trait data not associated with natural history information provide an incomplete picture of an organism's role in the ecosystem. Using data on the relative trophic position of 592 ant (Formicidae) samples comprising 393 species from 11 subfamilies and 19 widely distributed communities, we tested the extent to which commonly used functional proxies (i.e., morphometric traits) predict diet/trophic position as estimated from stable isotopes (δ15N). We chose ants as a group due to their ubiquity and abundance, as well as the wealth of available data on species traits and trophic levels. We measured 12 traits that have previously been identified as functionally significant, and corrected trait values for size and evolutionary history by using phylogenetically corrected trait residuals. Estimated trophic positions varied from 0.9 to 4.8 or roughly 4 trophic levels. Morphological data spanned nearly the entire size range seen in ants from the smallest (e.g., Strumigenys mitis total length 1.1 mm) to the largest species (e.g., Dinoponera australis total length 28.3 mm). We found overall body size, relative eye position, and scape length to be informative for predicting diet/trophic position in these communities, albeit with relatively weak predictive values. Specifically, trophic position was negatively correlated with body size and positively correlated with sensory traits (higher eye position and scape length). Our results suggest that functional trait-based approaches can be informative but should be used with caution unless clear links between form and function have been established.

When origin, reproduction ability and diet define the role of birds in invasions

The ecological impacts of invasive alien species (IAS) are increasingly documented; however, they are usually studied through the lens of either the IAS or the affected species (IAS-threatened species). A clear understanding of how both protagonists of biological invasions are characterized is still lacking. We investigated the morphology, life history and ecology of birds involved in biological invasions. Evaluating the distribution of 450 IAS-threatened birds and 400 alien birds in a functional space, we found that both groups retained various strategies. Aliens had larger clutches and were more likely to be herbivores than IAS-threatened and worldwide birds, while IAS-threatened birds were more insular endemic from the Australia region than alien and worldwide birds. IAS-threatened species showed opposite strategies to aliens regarding traits related to diet, origin and reproduction. Further comparing traits associated with impact magnitude, we found that even if aliens were mostly herbivorous, those with high impact had more a generalist behaviour and an animal-based diet compared to aliens with low impact. By emphasizing differences relating to the distribution of bird groups in a functional space, we opened new opportunities to identify the role of birds in biological invasions.

Traits shaping urban tolerance in birds differ around the world

As human density increases, biodiversity must increasingly co-exist with urbanization or face local extinction. Tolerance of urban areas has been linked to numerous functional traits, yet few globally consistent patterns have emerged to explain variation in urban tolerance, which stymies attempts at a generalizable predictive framework. Here, we calculate an Urban Association Index (UAI) for 3,768 bird species in 137 cities across all permanently inhabited continents. We then assess how this UAI varies as a function of ten species-specific traits and further test whether the strength of trait relationships vary as a function of three city-specific variables. Of the ten species traits, nine were significantly associated with urban tolerance. Urban-associated species tend to be smaller, less territorial, have greater dispersal ability, broader dietary and habitat niches, larger clutch sizes, greater longevity, and lower elevational limits. Only bill shape showed no global association with urban tolerance. Additionally, the strength of several trait relationships varied across cities as a function of latitude and/or human population density. For example, the associations of body mass and diet breadth were more pronounced at higher latitudes, while the associations of territoriality and longevity were reduced in cities with higher population density. Thus, the importance of trait filters in birds varies predictably across cities, indicating biogeographic variation in selection for urban tolerance that could explain prior challenges in the search for global patterns. A globally informed framework that predicts urban tolerance will be integral to conservation as increasing proportions of the world's biodiversity are impacted by urbanization.

Reconstructing the dietary habits and trophic positions of the Longipterygidae (Aves: Enantiornithes) using neontological and comparative morphological methods

The Longipterygidae are a unique clade among the enantiornithines in that they exhibit elongate rostra (≥60% total skull length) with dentition restricted to the distal tip of the rostrum, and pedal morphologies suited for an arboreal lifestyle (as in other enantiornithines). This suite of features has made interpretations of this group’s diet and ecology difficult to determine due to the lack of analogous taxa that exhibit similar morphologies together. Many extant bird groups exhibit rostral elongation, which is associated with several disparate ecologies and diets (e.g., aerial insectivory, piscivory, terrestrial carnivory). Thus, the presence of rostral elongation in the Longipterygidae only somewhat refines trophic predictions of this clade. Anatomical morphologies do not function singularly but as part of a whole and thus, any dietary or ecological hypothesis regarding this clade must also consider other features such as their unique dentition. The only extant group of dentulous volant tetrapods are the chiropterans, in which tooth morphology and enamel thickness vary depending upon food preference. Drawing inferences from both avian bill proportions and variations in the dental morphology of extinct and extant taxa, we provide quantitative data to support the hypothesis that the Longipterygidae were animalivorous, with greater support for insectivory.

Quantitative investigation of pengornithid enantiornithine diet reveals macrocarnivorous ecology evolved in birds by Early Cretaceous

The diet of Mesozoic birds is poorly known, limiting evolutionary understanding of birds' roles in modern ecosystems. Pengornithidae is one of the best understood families of Mesozoic birds, hypothesized to eat insects or only small amounts of meat. We investigate these hypotheses with four lines of evidence: estimated body mass, claw traditional morphometrics, jaw mechanical advantage, and jaw finite element analysis. Owing to limited data, the diets of Eopengornis and Chiappeavis remain obscure. Pengornis, Parapengornis, and Yuanchuavis show adaptations for vertebrate carnivory. Pengornis also has talons similar to living raptorial birds like caracaras that capture and kill large prey, which represents the earliest known adaptation for macrocarnivory in a bird. This supports the appearance of this ecology ∼35 million years earlier than previously thought. These findings greatly increase the niche breadth known for Early Cretaceous birds, and shift the prevailing view that Mesozoic birds mainly occupied low trophic levels.

Allometry reveals trade-offs between Bergmann's and Allen's rules, and different avian adaptive strategies for thermoregulation

Animals tend to decrease in body size (Bergmann's rule) and elongate appendages (Allen's rule) in warm climates. However, it is unknown whether these patterns depend on each other or constitute independent responses to the thermal environment. Here, based on a global phylogenetic comparative analysis across 99.7% of the world's bird species, we show that the way in which the relative length of unfeathered appendages co-varies with temperature depends on body size and vice versa. First, the larger the body, the greater the increase in beak length with temperature. Second, the temperature-based increase in tarsus length is apparent only in larger birds, whereas in smaller birds, tarsus length decreases with temperature. Third, body size and the length of beak and tarsus interact with each other to predict the species' environmental temperature. These findings suggest that the animals' body size and shape are products of an evolutionary compromise that reflects distinct alternative thermoregulatory adaptations.

Comprehensive Comparative Analysis Sheds Light on the Patterns of Microsatellite Distribution across Birds Based on the Chromosome-Level Genomes

Microsatellites (SSRs) are widely distributed in the genomes of organisms and are an important genetic basis for genome evolution and phenotypic adaptation. Although the distribution patterns of microsatellites have been investigated in many phylogenetic lineages, they remain unclear within the morphologically and physiologically diverse avian clades. Here, based on high-quality chromosome-level genomes, we examined the microsatellite distribution patterns for 53 birds from 16 orders. The results demonstrated that each type of SSR had the same ratio between taxa. For example, the frequency of imperfect SSRs (I-SSRs) was 69.90-84.61%, while perfect SSRs (P-SSRs) were 14.86-28.13% and compound SSRs (C-SSRs) were 0.39-2.24%. Mononucleotide SSRs were dominant for perfect SSRs (32.66-76.48%) in most bird species (98.11%), and A(n) was the most abundant repeat motifs of P-SSRs in all birds (5.42-68.22%). Our study further confirmed that the abundance and diversity of microsatellites were less effected by evolutionary history but its length. The number of P-SSRs decreased with increasing repeat times, and longer P-SSRs motifs had a higher variability coefficient of the repeat copy number and lower diversity, indicating that longer motifs tended to have more stable preferences in avian genomes. We also found that P-SSRs were mainly distributed at the gene ends, and the functional annotation for these genes demonstrated that they were related to signal transduction and cellular process. In conclusion, our research provided avian SSR distribution patterns, which will help to explore the genetic basis for phenotypic diversity in birds.

Convergence and contingency in the evolution of a specialized mode of life: multiple origins and high disparity of rock-boring bivalves

Evolutionary adaptation to novel, specialized modes of life is often associated with a close mapping of form to the new function, resulting in narrow morphological disparity. For bivalve molluscs, endolithy (rock-boring) has biomechanical requirements thought to diverge strongly from those of ancestral functions. However, endolithy in bivalves has originated at least eight times. Three-dimensional morphometric data representing 75 species from approximately 94% of extant endolithic genera and families, along with 310 non-endolithic species in those families, show that endolithy is evolutionarily accessible from many different morphological starting points. Although some endoliths appear to converge on certain shell morphologies, the range of endolith shell form is as broad as that belonging to any other bivalve substrate use. Nevertheless, endolithy is a taxon-poor function in Bivalvia today. This limited richness does not derive from origination within source clades having significantly low origination or high extinction rates, and today's endoliths are not confined to low-diversity biogeographic regions. Instead, endolithy may be limited by habitat availability. Both determinism (as reflected by convergence among distantly related taxa) and contingency (as reflected by the endoliths that remain close to the disparate morphologies of their source clades) underlie the occupation of endolith morphospace.