Convergence, adaptation, and constraint

Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales

Many specialized metabolic pathways have evolved convergently in plants, but distinguishing multiple origins from alternative evolutionary scenarios can be difficult. Here, we explore the evolution of l-3,4-dihydroxyphenylalanine (l-DOPA) 4,5-dioxygenase (DODA) enzymes to better resolve the convergent evolution of the betalain biosynthetic pathway within the flowering plant order Caryophyllales. We use yeast-based heterologous assays to quantify enzymatic activity of extant proteins and then employ ancestral sequence reconstruction to resurrect and assay ancestral DODA enzymes. We use a combination of ancestral sequence reconstruction, model-based methods, and structural modelling to describe patterns of molecular convergence. We confirm that high l-DOPA 4,5-dioxygenase activity is polyphyletic and show that high activity DODAs evolved at least three times from ancestral proteins with low activity. We show that molecular convergence is concentrated proximally to the binding pockets but also appears distally to active sites. Moreover, our analysis also suggests that many unique and divergent substitutions contribute to the evolution of DODA. Given the key role of DODA in betalain biosynthesis, our analysis further supports the convergent origins of betalains and illustrates how the iterative evolution of betalain biosynthesis has drawn on a complex mixture of convergent, divergent, and unique variation.

Strong bat predation and weak environmental constraints predict longer moth tails

Elaborate traits evolve via intense selective pressure, overpowering ecological constraints. Hindwing tails that thwart bat attack have repeatedly originated in moon moths (Saturniidae), with longer tails having greater anti-predator effect. Here, we take a macroevolutionary approach to evaluate the evolutionary balance between predation pressure and possible limiting environmental factors on tail elongation. To trace the evolution of tail length across time and space, we inferred a time-calibrated phylogeny of the entirely tailed moth group (Actias + Argema) and performed ancestral state reconstruction and biogeographical analyses. We generated metrics of predation via estimates of bat abundance from nearly 200 custom-built species distribution models and environmental metrics via estimates of bioclimatic variables associated with individual moth observations. To access community science data, we developed a novel method for measuring wing lengths from un-scaled photos. Integrating these data into phylogenetically informed mixed models, we find a positive association between bat predation pressure and moth tail length and body size, and a negative association between environmental factors and these morphological traits. Regions with more insectivorous bats and more consistent temperatures tend to host longer-tailed moths. Our study provides insight into tradeoffs between biotic selective pressures and abiotic constraints that shape elaborate traits across the tree of life.

Convergent Isobilateral Leaves Increase the Risk for Mangroves Facing Human-Induced Rapid Environmental Changes

Understanding plant adaptations in extreme environments is crucial, as these adaptations often confer advantages for survival. However, a significant gap exists regarding the genetic mechanisms underlying these adaptations and their responses to human-induced rapid environmental change (HIREC). This study addresses the question of whether genetic convergence occurs among plants with similar adaptive features, specifically focusing on isobilateral leaves in mangrove species. Here, we analyse the genetic convergence of isobilateral leaves in mangroves that have independently adapted to coastal intertidal zones. Our findings reveal that genetic convergence is evident in gene families involved in leaf abaxial and adaxial development, with strong selection pressures identified in photosynthesis and leaf polarity pathways. Despite these adaptations, mangrove species with isobilateral leaves occupy narrower ecological niches and face diminishing suitable habitat areas projected under various HIREC scenarios. These results indicate that while convergent traits enhance local adaptation, they may also increase vulnerability to ongoing environmental changes. This research provides valuable insight into the interplay between genetic adaptation and environmental resilience, underscoring the necessity for targeted biodiversity conservation strategies that safeguard specific adaptive traits amid rapid environmental shifts.

Trophic convergence of marine vertebrate communities worldwide

Biogeographic regions arise due to constraints on species ranges, fostering lineage divergence as a result. Yet, convergent evolution means that evolutionary distinct lineages can share similar characteristics when subjected to similar environmental conditions. The ecological convergence of distinct regions has been demonstrated in terrestrial communities, but it remains uncertain if marine systems exhibit similar patterns, given the greater ease of dispersal in the ocean. Using information on the dietary preferences of marine vertebrates, we develop an ocean regionalization that groups regions with similar trophic communities, describing how species are organized into trophic guilds and how guilds overlap with one another. Six types of trophic communities emerge globally, largely explained by temperature, productivity, and depth. Regions with analogous environments support similar numbers of species with analogous feeding strategies, even if the species do not share the same evolutionary origins. These findings support the notion that independently evolving sets of marine species can converge into functionally analogous trophic communities when exposed to similar environmental conditions. They also provide a benchmark for studying the functional consequences of global environmental change.

Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids

Cichlid fishes inhabiting the East African Great Lakes, Victoria, Malawi, and Tanganyika, are textbook examples of parallel evolution, as they have acquired similar traits independently in each of the three lakes during the process of adaptive radiation. In particular, 'hypertrophied lip' has been highlighted as a prominent example of parallel evolution. However, the underlying molecular mechanisms remain poorly understood. In this study, we conducted an integrated comparative analysis between the hypertrophied and normal lips of cichlids across three lakes based on histology, proteomics, and transcriptomics. Histological and proteomic analyses revealed that the hypertrophied lips were characterized by enlargement of the proteoglycan-rich layer, in which versican and periostin proteins were abundant. Transcriptome analysis revealed that the expression of extracellular matrix-related genes, including collagens, glycoproteins, and proteoglycans, was higher in hypertrophied lips, regardless of their phylogenetic relationships. In addition, the genes in Wnt signaling pathway, which is involved in promoting proteoglycan expression, was highly expressed in both the juvenile and adult stages of hypertrophied lips. Our comprehensive analyses showed that hypertrophied lips of the three different phylogenetic origins can be explained by similar proteomic and transcriptomic profiles, which may provide important clues into the molecular mechanisms underlying phenotypic parallelisms in East African cichlids.

Craniofacial modularity and the evolution of cranial kinesis in the adaptive radiation of Furnariidae (Aves: Passeriformes)

The role of phenotypic modularity in the evolution of skull morphology in birds has been a subject of debate in recent years. Furnariids (ovenbirds and woodcreepers), a spectacular avian adaptive radiation, are distinguished in their cranial morphology as the only passerines with two types of cranial kinesis, constituting a great model to test whether the evolution of novelties linked to kinesis was associated with shifts in patterns of evolutionary modularity and allometry in the avian skull. Our analyses by means of geometric morphometric tools and phylogenetic comparative methods show that the beak and neurocranium of furnariids evolved in a modular fashion and shaped by the cranial kinesis evolution. Besides, species with prokinesis show a higher degree of modularity and morphological disparity, lower phenotypic rates, as well as higher contribution of allometry in the evolution of the beak morphology than species with proximal rhynchokinesis, suggesting, as observed in several vertebrates, that the functional demands associated with higher degrees of cranial kinesis promoted rapid integration throughout the skull. Prokinetic-robust morphotypes and proximal rhynchokinetic-gracile morphotypes, have repeatedly evolved by evolutionary convergence in both modules, which suggests the existence of functional trade-offs and long-standing adaptive optima related to cranial kinesis.

Contrasting levels of transcriptome-wide SNP diversity and adaptive molecular variation among conifers

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are archaic species of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species (118 individuals from 67 populations) populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. The analysis of sequence homology also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of ~350 Mya between conifers and Angiosperms, we also uncovered a set of 17 key genes presumably under positive selection in both lineages.

Ontogenetic trajectories and sexual dimorphism of a neotropical ground snake genus Erythrolamprus (Serpentes: Dipsadidae)

Allometry and sexual dimorphism are potential sources of intraspecific morphological variation. Advances in the methodological framework of geometric morphometrics allow in-depth analysis of these issues, enabling the descriptions and comparisons between groups of multivariate phenotypic attributes and the visualization of allometric trajectories. In the present study, we evaluated the presence of secondary sexual dimorphism in Erythrolamprus miliaris merremi, a semi-aquatic snake occurring in the Atlantic Forest of southeastern Brazil. We assessed linear body measurements and digitized landmarks in the dorsal view of the head of 107 specimens grouped into four categories combining ontogenetic stages and sex. We performed linear models and principal component analyses to estimate and visualize head shape variation and the allometric trajectories of these categories. Adults from both sexes and immature females showed significant static allometry, while immature males showed isometric growth. Although we recovered no sexual dimorphism for head shape, ontogenetic trajectories of both sexes are distinct, with females showing head shape variation throughout ontogenetic development, while males exhibited more conspicuous changes only after sexual maturity. Comparisons with literature data suggest a high degree of variation in ontogenetic allometry of snakes, depending on the phylogenetic group or structure (head/skull) analyzed, while the results for static allometry are more similar between the studied taxa. Only the collection of data on distinct groups of snakes will provide more clues as to whether there is any allometric pattern to these structures, and which factors (evolutionary, ecological or both) are prevalent over it, especially for ontogenetic allometry.

Comparative tissue-specific transcriptomics reveals the regulatory control of convergent seed shattering in independently evolved weedy rice lineages

The repeated evolution of high seed shattering during multiple independent de-domestications of cultivated Asian rice (Oryza sativa) into weedy rice (Oryza spp.) is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low-shattering cultivars of aus and temperate japonica domesticated groups and in two genotypes of their derived high-shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de-domestication of SWR than BHA, fewer genes exhibited a comparable AZ-region exclusive expression pattern between weed and crop in the temperate japonica lineage than in the aus lineage. Transcription factors related to the repression of lignin and secondary cell wall deposition, such as, OsWRKY102 and OsXND-1-like, along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ-region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages.

Comparative genomics uncovers evolutionary drivers of locust migratory adaptation

BACKGROUND

Locust migration is one of the main causes of locust plagues. While existing research has highlighted the adaptive migratory capabilities of locusts, the evolutionary patterns of their migration remain elusive. This study aims to explore these evolutionary patterns of locust migratory behavior at the genomic level. To achieve this, we conducted comparative genomics analysis using genomic data from 10 locust species with diverse migratory tendencies.

RESULTS

We identified 1064 genes showing signatures of positive selection in five migratory locust species using a dN/dS model. The BUSTED-PH model revealed 116 genes associated with migratory phenotypes. Gene ontology enrichment analysis indicated that these genes were predominantly related to metabolism and mitochondria-related pathways through both methods. Additionally, the evolutionary rate (RER) analysis between migratory and non-migratory locusts revealed significant divergence in energy metabolism pathways. Notably, of the genes analyzed, the SETX gene consistently showed evidence of positive selection across all five migratory species.

CONCLUSIONS

The findings suggest that the evolution of migratory behavior is associated with increased selective pressure on metabolism and mitochondria-related pathways. Hundreds of genes undergo selective changes during repetitive transitions to migratory behavior. These findings enhance our understanding of the genetic and phenotypic relationships underlying different locust migratory behaviors, providing important data for understanding the biological mechanisms behind locust outbreaks.

Exploring shape diversity and sexual dimorphism in two populations of Nigma conducens through geometric morphometrics

BACKGROUND

Spiders are highly adaptable hunters found in nearly all terrestrial ecosystems and play an important role in biological control by preying on pest insects. Spiders' body size and shape are vital for their survival, particularly in prey capture, and these morphological features are often utilized in cladistic analyses. This study employed geometric morphometrics to investigate prosoma shape and size variations between two populations of Nigma conducens spiders and between sexes within each population. Principal Component Analysis (PCA) explored shape variation, while Canonical Variate Analysis (CVA) compared shape differences between populations and sexes. Multivariate regression analysis was used to check for allometry.

RESULTS

MANOVA results revealed significant shape variations in spider prosoma between the two populations and between sexes, though the degree of these differences was small. The considerable overlap in individual shapes between populations may indicate a response to microhabitat similarity. Additionally, sexual dimorphism was observed in the prosoma shape of N. conducens, likely due to sexual selection or adaptive divergence related to different microhabitats. Size differences between sexes were insignificant in either population, particularly in the first, suggesting that prosoma size does not contribute to reproductive success. Moreover, the non-allometric relationship indicated that shape variations between the populations were independent of size.

CONCLUSION

Overall, these findings highlight the complexity of morphological adaptations in N. conducens in response to ecological pressures and sexual selection.

The Convergent Evolution of Hummingbird Pollination Results in Repeated Floral Scent Loss Through Gene Downregulation

The repeated evolution of the same trait in different lineages provides powerful natural experiments to study the phenotypic and genotypic predictability of trait gain and loss. A fascinating example is the repeated evolution of hummingbird pollination in plant lineages in the Americas, a widespread and often unidirectional phenomenon. The spiral gingers in the genus Costus are ancestrally bee pollinated, and hummingbird pollination has evolved multiple times independently in the tropical Americas. These pollinator transitions are accompanied by predictable morphological and color changes, but the changes in floral scent have not been described. In this study, we describe the floral scent composition of 30 species of Costus sampled across the phylogeny to understand how floral scent has evolved across the genus with respect to pollinator transitions. We then combine transcriptomics and genomics to identify gene expression differences and gene family evolution associated with pollinator transitions. We show that hummingbird-pollinated species have mostly lost their floral scent, whereas bee-pollinated species exhibit either floral scent maintenance or, in some cases, gains of more diverse scent profiles. We find the floral scent loss appears to be due to gene downregulation rather than pseudogenization. The remarkable consistency of scent loss in hummingbird-pollinated species highlights the shared strong selection pressures experienced by these lineages. Even species with more recent transitions from bee to hummingbird pollination exhibit scent loss, highlighting the rapid breakdown of scent emission following pollinator transitions. This research highlights the capacity for rapid changes when selection pressures are strong through downregulation of floral scent genes.

Transcriptomic Data Reveal Divergent Paths of Chitinase Evolution Underlying Dietary Convergence in Anteaters and Pangolins

Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, and hypertrophied salivary glands producing large amounts of saliva. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functional CHIA paralogs (CHIA1-4), Asian pangolins (Manis spp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of different CHIA paralogs is observed in insectivorous species. Furthermore, convergently evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin, CHIA5 is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels for CHIA1 and CHIA2 in the pancreas and for CHIA3 and CHIA4 in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms within the chitinase acidic gene family underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin digestive enzyme toolkit in this classic example of convergent evolution.

Phylogenetic Perspectives and Ethnobotanical Insights on Wild Edible Plants of the Mediterranean, Middle East, and North Africa

This study investigates the phylogenetic and geographical distribution of wild food plants (WFPs) across 30 Mediterranean and North African (MENA) regions, focusing on the intersection of evolutionary lineage, ecological adaptation, and cultural utilization. A phylogenetic analysis of 111 genera of WFPs used in traditional diets reveals clusters reflecting shared ancestry, functional adaptations, and ecological resilience. Key regions such as Lebanon and Ikaria stand out as potential centers for the diversity of wild food plant use, suggesting that the Eastern Mediterranean may be a primary origin area, especially for species adapted to semi-arid climates. Major plant families including Lamiaceae, Rosaceae, and Fabaceae form distinct clusters that underscore their common ancestry and adaptability, making them foundational to traditional diets and medicinal applications across various environments. Geographical analysis indicates historical connections, such as those between Malta and Egypt, supporting the hypothesis that ancient trade routes influenced the spread and cultural exchange of wild food plant use across the Mediterranean. The study emphasizes the integration of phylogenetic and ethnobotanical perspectives, shedding light on how biodiversity, ecological adaptation, and cultural practices intersect in these regions. This research demonstrates that WFPs serve as both ecological and cultural assets, crucial for preserving traditional diets and supporting biodiversity conservation amid environmental changes. Integrating evolutionary and cultural knowledge can enrich ecological understanding and contribute to the sustainable use of plant resources in the MENA regions.

Convergent Gene Duplication in Arctic and Antarctic Teleost Fishes

Teleost fishes have independently colonized polar regions multiple times, facing many physiological and biochemical challenges due to frigid temperatures. Although increased gene copy numbers can contribute to adaptive evolution in extreme environments, it remains unclear which categories of genes exhibit increased copy numbers associated with polar colonization. Using 104 species of ray-finned fishes, we systematically identified genes with a significant correlation between copy number and polar colonization after phylogenetic correction. Several genes encoding extracellular glycoproteins, including zona pellucida (ZP) proteins, which increase their copy number in Antarctic notothenioid fishes, exhibited elevated copy numbers across multiple polar fish lineages. Additionally, some genes reported to be highly expressed under cold stress, such as cold-inducible RNA-binding protein (CIRBP), had significantly increased copy numbers in polar fishes. Further analysis will provide a fundamental basis for understanding the role of gene duplication in polar adaptations.

Repeated evolution of photoperiodic plasticity by different genetic architectures during recurrent colonizations in a butterfly

In cases of recurrent colonizations of similar habitats from the same base population, it is commonly expected that repeated phenotypic adaptation is caused by parallel changes in genetic variation. However, it is becoming increasingly clear that similar phenotypic variation may also evolve by alternative genetic pathways. Here, we explore the repeated evolution of photoperiodic plasticity for diapause induction across Swedish populations of the speckled wood butterfly, Pararge aegeria. This species has colonized Scandinavia at least twice, and population genomic results show that one of the candidate regions associated with spatial variation in photoperiodism is situated on the Z-chromosome. Here, we assay hybrid crosses between several populations that differ in photoperiodic plasticity for sex-linked inheritance of the photoperiodic reaction norm. We find that while a cross between more distantly related populations from the two different colonization events shows strong sex-dependent inheritance of photoperiodic plasticity, a cross between two more closely related populations within the oldest colonization range shows no such effect. We conclude that the genotype-phenotype map for photoperiodic plasticity varies across these populations and that similar local phenotypic adaptation has evolved during recurrent colonization events by partly non-parallel genetic changes.

Divergence time and environmental similarity predict the strength of morphological convergence in stick and leaf insects

Independent evolution of similar traits in lineages inhabiting similar environments (convergent or repeated evolution) is often taken as evidence for adaptation by natural selection, and used to illustrate the predictability of evolution. Yet convergence is rarely perfect for two reasons. First, environments may not be as similar as they appear. Second, responses to selection are contingent upon available genetic variation and independent lineages may differ in the alleles, genetic backgrounds, and even the developmental mechanisms responsible for the phenotypes in question. Both impediments to convergence are predicted to increase as the length of time separating two lineages increases, making it difficult to discern their relative importance. We quantified environmental similarity and the extent of convergence to show how habitat and divergence time each contribute to observed patterns of morphological evolution in 212 species of stick and leaf insects (order Phasmatodea). Dozens of phasmid lineages independently colonized similar habitats, repeatedly evolving in parallel directions on a 23-trait morphospace, though the magnitude and direction of these shifts varied. Lineages converging toward more similar environments ended up closer on the morphospace, as did closely related lineages, and closely related lineages followed more parallel evolutionary trajectories to arrive there than more distantly related ones. Remarkably, after accounting for habitat similarity, we show that divergence time reduced the extent of convergence at a constant rate across more than 100 My of separation, suggesting even the magnitude of contingency can be predictable, given sufficient spans of time.

Modulating vertebrate physiology by genomic fine-tuning of GPCR functions

G protein-coupled receptors (GPCRs) play a crucial role as membrane receptors, facilitating the communication of eukaryotic species with their environment and regulating cellular and organ interactions. Consequently, GPCRs hold immense potential in contributing to adaptation to ecological niches and responding to environmental shifts. Comparative analyses of vertebrate genomes reveal patterns of GPCR gene loss, expansion, and signatures of selection. Integrating these genomic data with insights from functional analyses of gene variants enables the interpretation of genotype-phenotype correlations. This review underscores the involvement of GPCRs in adaptive processes, presenting numerous examples of how alterations in GPCR functionality influence vertebrate physiology or, conversely, how environmental changes impact GPCR functions. The findings demonstrate that modifications in GPCR function contribute to adapting to aquatic, arid, and nocturnal habitats, influencing camouflage strategies, and specializing in particular dietary preferences. Furthermore, the adaptability of GPCR functions provides an effective mechanism in facilitating past, recent, or ongoing adaptations in animal domestication and human evolution and should be considered in therapeutic strategies and drug development.

Dormancy in the origin, evolution and persistence of life on Earth

Life has existed on Earth for most of the planet's history, yet major gaps and unresolved questions remain about how it first arose and persisted. Early Earth posed numerous challenges for life, including harsh and fluctuating environments. Today, many organisms cope with such conditions by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This process protects inactive individuals and minimizes the risk of extinction by preserving information that stabilizes life-system dynamics. Here, we develop a framework for understanding dormancy on early Earth, beginning with a primer on dormancy theory and its core criteria. We hypothesize that dormancy-like mechanisms acting on chemical precursors in a prebiotic world may have facilitated the origin of life. Drawing on evidence from phylogenetic reconstructions and the fossil record, we demonstrate that dormancy is prevalent across the tree of life and throughout deep time. These observations lead us to consider how dormancy might have shaped nascent living systems by buffering stochastic processes in small populations, protecting against large-scale planetary disturbances, aiding dispersal in patchy landscapes and facilitating adaptive radiations. Given that dormancy is a fundamental and easily evolved property on Earth, it is also likely to be a feature of life elsewhere in the universe.

Pollination ecotypes and the origin of plant species

Ecological niche shifts are a key driver of phenotypic divergence and contribute to isolating barriers among lineages. For many groups of organisms, the history of these shifts and associated trait-environment correlations are well-documented at the macroevolutionary level. However, the processes that generate these patterns are initiated below the species level, often by the formation of ecotypes in contrasting environments. Here, I review the evidence in plants for 'pollination ecotypes' as microevolutionary responses to environmental gradients in pollinator availability. Pollinators are critical for population establishment and persistence in most species, thereby forming part of their fundamental niche. Novel floral trait combinations allow species to exploit particular pollination opportunities in local habitats and evolve primarily through sexual selection due to their effects on mating success. I examine selected case studies on the evolution of pollination ecotypes, including self-pollinating forms, and use these to illustrate challenging practical and conceptual issues. These issues include the paucity of reliable natural history data, the problem of implementing and interpreting reciprocal translocation experiments, and establishing criteria for when allopatric ecotypes should be considered species.

Adaptive or non-adaptive? Cranial evolution in a radiation of miniaturized day geckos

Lygodactylus geckos represent a well-documented radiation of miniaturized lizards with diverse life-history traits that are widely distributed in Africa, Madagascar, and South America. The group has diversified into numerous species with high levels of morphological similarity. The evolutionary processes underlying such diversification remain enigmatic, because species live in different ecological biomes, ecoregions and microhabitats, while suggesting strikingly high levels of homoplasy. To underscore this evolutionary pattern, here we explore the shape variation of skull elements (i.e., cranium, jaw and inner ear) using 3D geometric morphometrics and phylogenetic comparative methods on computed tomography scans (CT-scan) of a sample encompassing almost all recognized taxa within Lygodactylus. The results of this work show that skull and inner ear shape variation is low (i.e., there is high overlapping on the morphospace) across geographic regions, macrohabitats and lifestyles, implying extensive homoplasy. Furthermore, we also found a strong influence of allometry shaping cranial variation both at intra and interspecific levels, suggesting a major constraint underlying skull architecture, probably as a consequence of its miniaturization. The remaining variation that is not allometric is independent of phylogeny and ecological adaptation and can probably be interpreted as the result of intrinsic developmental plasticity. This, in turn, supports the interpretation that speciation in this group is largely concordant with a non-adaptive hypothesis, which results mainly from vicariant processes.

Widespread adaptive evolution in angiosperm photosystems provides insight into the evolution of photosystem II repair

Oxygenic photosynthesis generates the initial energy source that fuels nearly all life on Earth. At the heart of the process are the photosystems, which are pigment binding multiprotein complexes that catalyze the first step of photochemical conversion of light energy into chemical energy. Here, we investigate the molecular evolution of the plastid-encoded photosystem subunits at single-residue resolution across 773 angiosperm species. We show that despite an extremely high level of conservation, 7% of residues in the photosystems, spanning all photosystem subunits, exhibit hallmarks of adaptive evolution. Through in silico modeling of these adaptive substitutions, we uncover the impact of these changes on the predicted properties of the photosystems, focusing on their effects on cofactor binding and intersubunit interface formation. By analyzing these cohorts of changes, we reveal that evolution has repeatedly altered the interaction between Photosystem II and its D1 subunit in a manner that is predicted to reduce the energetic barrier for D1 turnover and photosystem repair. Together, these results provide insight into the trajectory of photosystem adaptation during angiosperm evolution.

Insight Into Body Size Evolution in Aves: Based on Some Body Size-Related Genes

Birds exhibit remarkable variations in body size, making them an ideal group for the study of adaptive evolution. However, the genetic mechanisms underlying body size evolution in avian species remain inadequately understood. This study investigates the evolutionary patterns of avian body size by analyzing 15 body-size-related genes, including GHSR, IGF2BP1, and IGFBP7 from the growth hormone/insulin-like growth factor axis, EIF2AK3, GALNS, NCAPG, PLOD1, and PLAG1 associated with tall stature, and ACAN, OBSL1, and GRB10 associated with short stature, four genes previously reported in avian species: ATP11A, PLXDC2, TNS3, and TUBGCP3. The results indicate significant adaptive evolution of body size-related genes across different avian lineages. Notably, in the IGF2BP1 gene, a significant positive correlation was observed between the evolutionary rate and body size, suggesting that larger bird species exhibit higher evolutionary rates of the IGF2BP1 gene. Furthermore, the IGFBP7 and PLXDC2 genes demonstrated accelerated evolution in large- and medium-sized birds, respectively, indicating distinct evolutionary patterns for these genes among birds of different sizes. The branch-site model analysis identified numerous positively selected sites, primarily concentrated near functional domains, thereby reinforcing the critical role of these genes in body size evolution. Interestingly, extensive convergent evolution was detected in lineages with larger body sizes. This study elucidates the genetic basis of avian body size evolution for the first time, identifying adaptive evolutionary patterns of body size-related genes across birds of varying sizes and documenting patterns of convergent evolution. These findings provide essential genetic data and novel insights into the adaptive evolution of body size in birds.

Morphological complexity promotes origination and extinction rates in ammonoids

The causes of heterogeneity in evolutionary rates are a key question in macroevolution. Origination and extinction rates are closely related to abiotic factors, such as climate1,2 and geography,3,4 as well as biotic factors such as taxonomic richness5,6 and morphology,7 which are influenced by phylogeny.8,9 Studies on the relationship between morphology and macroevolution have focused on morphological traits, including body size,6,7,9 shape,10 color,11,12 and complexity,13,14,15 and have proposed biological laws, such as the zero-force evolutionary law16 and Cope's rule.17 However, the relationship between morphological complexity and turnover rates remains poorly defined because of the lack of suitable measures for various subjects.18,19 Here, we establish a quantitative method, the two-dimensional ornamentation index (2D-OI), which allows the description of the ornamental complexity of ammonoids. Ammonoids are one of the most abundant and well-studied fossil groups, with complex conch structures.20 Ammonoids display some similarities with trilobites and mammals21,22 in terms of their high evolutionary rates; however, the underlying mechanisms remain elusive. Moreover, ammonoids exhibit marked heterogeneity in turnover rates across spatiotemporal scales23 and clades,23,24 making them key clades for investigating the relationship between turnover rates and morphological complexity. The results show that morphologically complex genera and species often have higher origination and extinction rates than morphologically simple taxa. Diversity fluctuations of taxa with complex ornamentation generally overimprint and control the overall net diversification rates of ammonoids. This double-edged sword of rapid evolution and increased extinction risk driven by complex morphologies has significant implications for our understanding of how species survive over geological timescales.

Do It Well or Not at All: Alternative Flight Solutions for Alpine Insects

Exposed and isolated alpine ecosystems present evolutionary challenges for flying species worldwide. Many insects have undergone dramatic wing reduction in response to these harsh conditions, losing the ability to fly. By contrast, some taxa have countered alpine conditions by evolving larger wings to improve flight ability. In this study, we investigated how two independent clades of Zelandoperla fenestrata stoneflies respond to upland environments. Our results revealed strikingly different adaptations to elevation across the two closely related clades. In Clade 1 (southern South Island), wing length decreases sharply with increasing elevation. In contrast, wing length in the geographically adjacent Clade 2 (northern South Island, and North Island) increases with elevation. These contrasting strategies highlight the diverse adaptive pathways that may exist even for closely related lineages encountering similar environmental challenges.

Burrowing Constrains the Phenotypic Diversity of Fossorial Crayfish

Strong selective pressure on phenotype can arise when habitat transitions fundamentally alter the physical media in which animals live, such as the invasion of land by lobe-finned fishes and insects. When environmental gradients differ drastically among habitats and multiple lineages transition between these habitats, we expect phenotypic convergence to be prevalent. One transition where widespread convergence has been observed is the shift from aboveground to subterranean environments in fossorial animals. Subterranean environments are low-light, confined spaces and tend to be hypoxic or anoxic, not to mention that the act of burrowing itself demands morphological specializations for excavation. Research suggests burrowing promotes morphological convergence in crayfish, with non-burrowing forms having a dorsoventrally compressed carapace and long, slender claws (chelae), while primary burrowing forms have a dorsolaterally compressed carapace and shorter, more powerful claws. However, earlier ecomorphological comparisons relied on qualitative rather than quantitative assessments of phenotypic differences. This study tested for convergence in North American crayfishes using a geometric morphometric approach. We photographed the carapace and claw for representative species across 13 North American genera. We hypothesized that crayfishes that occur in similar habitats and exhibit similar burrowing behaviors, would converge in their carapace and claw shapes. We found evidence for convergence in carapace and claw morphologies in burrowing crayfishes. However, claw phenotypes did not converge as strongly as carapace shape, an example of "imperfect" or "incomplete" convergence we attribute to the multiple competing demands on claw form and function. We argue that nuances in habitat characteristics, like soil type or compaction, make complete convergence unlikely for range- and dispersal-limited fossorial crayfishes.

Physiological Basis of Convergent Evolution in Animal Communication Systems

To humans, the diverse array of display behaviors that animals use for communication can easily seem peculiar or bizarre. While ample research delves into the evolutionary principles that shape these signals' effectiveness, little attention is paid to evolutionary patterning of signal design across taxa, particularly when it comes to the potential convergent evolution of many elaborate behavioral displays. By taking a mechanistic perspective, we explore the physiological and neurobiological mechanisms that likely influence the evolution of communication signals, emphasizing the utilization of pre-existing structures over novel adaptations. Central to this investigation are the concepts of perceptual bias and ritualization that we propose contribute to the convergence of elaborate display designs across species. Perceptual bias explains a phenomenon where pre-existing perceptual systems of receivers, used for innate behaviors such as food and predator recognition, select for certain traits of a communication signal from a signaler. Ritualization occurs when traits with no functional role in communication are co-opted through selection and transformed into a new communicative signal. Importantly, susceptibility for ritualization can be brought about through physiological modifications that occurred early in evolutionary time. In this way, perceptual bias can be a selective force that causes the co-option of non-communicative traits into a new communication signal through ritualization involving pre-existing modifications to physiological systems. If the perceptual bias, non-communicative signal, and physiological modifications that increase susceptibility to ritualization are highly conserved, then we may see the convergent evolution of the new communication signal with unrelated taxa facing similar sensory constraints. We explore this idea here using the foot-flagging frog system as a theoretical case study.

Does Phenotypic Integration Promote Convergent Evolution?

Phenotypic integration is often perceived as being able to produce convergent evolution in the absence of selection, but specific mechanisms for this process are lacking and a connection has never been empirically demonstrated. A new model of the effect of integration on convergence provides such a mechanism, along with other predictions about the influence of integration on evolutionary patterns. I use simulations and data from three empirical systems-turtle shells, characiform fish, and squirrel mandibles-to investigate the degree to which evolutionary integration is associated with high levels of convergent evolution. Levels of integration were varied in Brownian motion simulations and the resulting amounts of stochastic convergent evolution were quantified. Each empirical system was divided into modules, and the strength of integration, average amount of convergence, phenotypic disparity, and rate of evolution in each module were measured. Results from the simulations and from all three empirical systems converge on a common result: higher levels of phenotypic integration are indeed associated with higher levels of convergence. This is despite a lack of consistent association between the strength of phenotypic integration and evolutionary rate or disparity. The results here are only correlational. Further studies that more closely examine the influence of within-population drivers of evolutionary integration-for example, genetic or developmental integration-on convergence are required before it is possible to definitively establish when phenotypic integration can cause evolutionary convergence. Until then, however, the results of this study strongly suggest that phenotypic integration will often promote convergent evolution.

Phenotypic Convergence Is Stronger and More Frequent in Herbivorous Fishes

Constraints on phenotypic evolution can lead to patterns of convergent evolution, by limiting the "pool" of potential phenotypes in the face of endogenous (functional, developmental) or exogenous (competition, predation) selective pressures. Evaluation of convergence depends on integrating ecological and morphological data within a robust, comparative phylogenetic context. The staggering diversity of teleost fishes offers a multitude of lineages adapted for similar ecological roles and, therefore, offers numerous replicated evolutionary experiments for exploring phenotypic convergence. However, our understanding of fish feeding systems has been primarily shaped by marine species, with the monolithic exception of freshwater cichlids. Here we use piranhas and pacus (Serrasalmidae) to explore the evolution of different feeding ecologies and their morphological proxies in Neotropical freshwater environments. Specifically, we explore whether convergence is more widespread among plant-eating fishes, arising from strong constraints on phenotypic evolution in herbivores. Using osteological micro-computed tomographic imaging (μCT), we describe the major axes of morphological variation in pacus and piranhas, regarding their diet and feeding behaviors. Next, we evaluated whether herbivorous niches are less labile than other dietary guilds and whether herbivorous species' phenotypes evolve at a slower evolutionary rate than other taxa. We then assess how convergent herbivorous taxa are, using three different suites of morphological characters (dental, jaw, and abdominal morphometrics). Ecologically, herbivory is not a dead end, exhibiting similar observed transition rates as those between carnivores and omnivores. However, we documented widespread convergence in herbivores and that herbivores have slower rates of phenotypic evolution than carnivores. Most instances of convergence are found in herbivorous taxa, specifically in frugivores and folivores. Moreover, instances of "complete" convergence, indicated by positive convergence metrics observed in more than one morphometric dataset, were only found in herbivores. Herbivores do appear to evolve under constrained circumstances, but this has not limited their ecological ability.

Skull evolution and lineage diversification in endemic Malagasy carnivorans

Madagascar is one of the world's foremost biodiversity hotspots with more than 90% of its species endemic to the island. Malagasy carnivorans are one of only four extant terrestrial mammalian clades endemic to Madagascar. Although there are only eight extant species, these carnivorans exhibit remarkable phenotypic and ecological diversity that is often hypothesized to have diversified through an adaptive radiation. Here, we investigated the evolution of skull diversity in Malagasy carnivorans and tested if they exhibited characteristics of convergence and an adaptive radiation. We found that their skull disparity exceeds that of any other feliform family, as their skulls vary widely and strikingly capture a large amount of the morphological variation found across all feliforms. We also found evidence of shared adaptive zones in cranial shape between euplerid subclades and felids, herpestids and viverrids. Lastly, contrary to predictions of adaptive radiation, we found that Malagasy carnivorans do not exhibit rapid lineage diversification and only marginally faster rates of mandibular shape evolution and to a lesser extent cranial shape evolution, compared to other feliforms. These results reveal that exceptional diversification rates are not necessary to generate the striking phenotypic diversity that evolved in carnivorans after their dispersal to and isolation on Madagascar.

Signatures of convergence in Neotropical cichlid fish

Convergent evolution of similar phenotypes suggests some predictability in the evolutionary trajectories of organisms, due to strong and repeated selective pressures, and/or developmental constraints. In adaptive radiations, particularly in cichlid fish radiations, convergent phenotypes are commonly found within and across geographical settings. Cichlids show major repeated axes of morphological diversification. Recurrent changes in body patterns reveal adaption to alternative habitats, and modifications of the trophic apparatus respond to the exploitation of different food resources. Here we compare morphologically and genetically two Neotropical cichlid assemblages, the Mexican desert cichlid and the Nicaraguan Midas cichlid, with similar polymorphic body and trophic adaptations despite their independent evolution. We found a common morphological axis of differentiation in trophic structures in both cichlid radiations, but two different axes of differentiation in body shape, defining two alternative limnetic body patterns. Adaptation to limnetic habitats implied regulation of immune functions in the Midas cichlid, while morphogenesis and metabolic functions in the desert cichlid. Convergent phenotypic adaptions could be associated to divergent gene regulation.

Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.

A host driven parasitoid syndrome: Convergent evolution of multiple traits associated with woodboring hosts in Ichneumonidae (Hymenoptera, Ichneumonoidea)

The evolution of convergent phenotypes is of major interest in biology because of their omnipresence and ability to inform the study of evolutionary novelty and constraint. Convergent phenotypes can be combinations of traits that evolve concertedly, called syndromes, and these can be shaped by a common environmental pressure. Parasitoid wasps which use a wide variety of arthropod hosts have also repeatedly and convergently switched host use across their evolutionary history. They thus represent a natural laboratory for the evolution of trait syndromes that are associated with parasitism of specific hosts and host substrates. In this study, we tested the evolution of co-evolving characters in the highly diverse family Ichneumonidae associated with ovipositing in a specific and well-defined substrate: wood. Using a newly constructed phylogeny and an existing morphological dataset, we identified six traits correlated with the wood-boring lifestyle that demonstrate convergent evolution. At least one trait, the presence of teeth on the ovipositor, typically preceded the evolution of other traits and possibly the switch to parasitism of wood-boring hosts. For each trait, we provide a historical review of their associations with wood-boring parasitoids, reevaluate the function of some characters, and suggest future coding improvements. Overall, we demonstrate the convergent evolution of multiple traits associated with parasitism of woodboring hosts and propose a syndrome in a hyper diverse lineage of parasitoid wasps.

A repeatedly evolved mutation in Cryptochrome-1 of subterranean animals alters behavioral and molecular circadian rhythms

The repeated evolution of similar phenotypes in independent lineages often occurs in response to similar environmental pressures, through similar or different molecular pathways. Recently, a repeatedly occurring mutation R263Q in a conserved domain of the protein Cryptochrome-1 (CRY1) was reported in multiple species inhabiting subterranean environments. Cryptochromes regulate circadian rhythms, and glucose and lipid metabolism. Subterranean species show changes to their circadian rhythm and metabolic pathways, making it likely that this mutation in CRY1 contributes to adaptive phenotypic changes. To identify the functional consequences of the CRY1 R263Q mutation, we generated a mouse model homozygous for this mutation. Indirect calorimetry experiments revealed delayed energy expenditure, locomotor activity and feeding patterns of mutant mice in the dark phase, but no further metabolic phenotypes - unlike a full loss of function of CRY1. Gene expression analyses showed altered expression of several canonical circadian genes in the livers of the mutant mice, fortifying the notion that CRY1 R263Q impacts metabolism. Our data provide the first characterization of a novel mutation that has repeatedly evolved in subterranean environments, supporting the idea that shared environmental constraints can drive the evolution of similar phenotypes through similar genetic changes.

Shell biomechanics suggests an aquatic palaeoecology at the dawn of turtle evolution

The turtle shell is a remarkable structure that has intrigued not only evolutionary biologists but also engineering and material scientists because of its multi-scale complexity and various functions. Although protection is its most apparent role, the carapace and plastron are also related to many physiological functions and their shape influences hydrodynamics and self-righting ability. As such, analysing the functional morphology of the shell could help understanding the ecology of Triassic stem-turtles, which will contribute to the century-long debate on the evolutionary origins of turtles. Here, we used 3D imaging techniques to digitize the shells of two of the earliest stem-turtle taxa, Proganochelys and Proterochersis, and submitted their models to biomechanical and shape analyses. We analysed the strength performance under five predation scenarios and tested the function of two morphological traits found in stem-turtles, the epiplastral processes and an attached pelvic girdle. The latter, also present in the crown-lineage of side-necked turtles, has been suggested to increase load-bearing capacity of the shell or to improve swimming in pleurodires. Our results do not confirm the shell-strengthening hypothesis and, together with the results of our shape analyses, suggest that at least one of the first stem-turtles (Proterochersis) was an aquatic animal.

Physiology Evolves Convergently but Lags Behind Warming in Cities

Cities, through the generation of urban heat islands, provide a venue for exploring contemporary convergent evolution to climatic warming. We quantified how repeatable the evolution of heat tolerance, cold tolerance, and body size was among diverse lineages in response to urban heat islands. Our study revealed significant shifts toward higher heat tolerance and diminished cold tolerance among urban populations. We further found that the magnitude of trait divergence was significantly and positively associated with the magnitude of the urban heat island, suggesting that temperature played a major role in the observed divergence in thermal tolerance. Despite these trends, the magnitude of trait responses lagged behind environmental warming. Heat tolerance responses exhibited a deficit of 0.84°C for every 1°C increase in warming, suggesting limits on adaptive evolution and consequent adaptational lags. Other moderators were predictive of greater divergence in heat tolerance, including lower baseline tolerance and greater divergence in body size. Although terrestrial species did not exhibit systematic shifts toward larger or smaller body size, aquatic species exhibited significant shifts toward smaller body size in urban habitats. Our study demonstrates how cities can be used to address long-standing questions in evolutionary biology regarding the repeatability of evolution. Importantly, this work also shows how cities can be used as forecasting tools by quantifying adaptational lags and by developing trait-based associations with responses to contemporary warming.

Reconstructive evolutionary morphology: Tracing the historical process of modifications of complex systems driven by natural selection through changing ecological conditions

There is general consensus among evolutionary biologists that natural selection drives phenotypic modifications within populations over generational time. How to reconstruct this historical process, however, has been discussed mostly in theoretical terms, and recommendations and explanations on how to translate such theoretical insights into practice are needed. The present study aims at providing a theory-supported practical guide on how to reconstruct historical evolutionary processes by applying a morphology-centered approach through a series of interdependent steps of descriptive morphology, functional analysis, ecological observation, integration of paleoecological data, and evolutionary synthesis. Special attention is given to the development of tests regarding the accuracy, closeness to reality, and plausibility of the hypotheses at every level of the reconstructive process. This morphology-centered approach had its beginnings in the wake of the evolutionary synthesis and is part of the scientifically necessary process of reciprocal testing of hypotheses generated by different methods and data for the reconstruction of evolutionary history.

Convergence and Divergence among Herbivorous Insects Specialized on Toxic Plants: Revealing Syndromes among the Cardenolide Feeders across the Insect Tree of Life

AbstractRepeatable macroevolutionary patterns provide hope for rules in biology, especially when we can decipher the underlying mechanisms. Here we synthesize natural history, genetic adaptations, and toxin sequestration in herbivorous insects that specialize on plants with cardiac glycoside defenses. Work on the monarch butterfly provided a model for evolution of the "sequestering specialist syndrome," where specific amino acid substitutions in the insect's Na+/K+-ATPase are associated with (1) high toxin resistance (target site insensitivity [TSI]), (2) sequestration of toxins, and (3) aposematic coloration. We evaluate convergence for these traits within and between Lepidoptera, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Orthoptera, encompassing hundreds of toxin-adapted species. Using new and existing data on ∼28 origins of specialization, we show that the monarch model evolved independently in five taxonomic orders (but not Diptera). An additional syndrome occurs in five orders (all but Hymenoptera): aposematic sequesterers with modest to medium TSI. Indeed, all sequestering species were aposematic, and all but one had at least modest TSI. Additionally, several species were aposematic nonsequesterers (potential Batesian mimics), and this combination evolved in species with a range of TSI levels. Finally, we identified some biases among these strategies within taxonomic orders. Biodiversity in this microcosm of life evolved repeatedly with a high degree of similarity across six taxonomic orders, yet we identified alternative trait combinations as well as lineage-specific outcomes.

Competing adaptations maintain nonadaptive variation in a wild cricket population

How emerging adaptive variants interact is an important factor in the evolution of wild populations, but the opportunity to empirically study this interaction is rare. We recently documented the emergence of an adaptive phenotype "curly-wing" in Hawaiian populations of field crickets (Teleogryllus oceanicus). Curly-wing inhibits males' ability to sing, protecting them from eavesdropping parasitoid flies (Ormia ochracea). Surprisingly, curly-wing co-occurs with similarly protective silent "flatwing" phenotypes in multiple populations, in which neither phenotype has spread to fixation. These two phenotypes are frequently coexpressed, but since either sufficiently reduces song amplitude to evade the fly, their coexpression confers no additional fitness benefit. Numerous "off-target" phenotypic changes are known to accompany flatwing, and we find that curly-wing, too, negatively impacts male courtship ability and affects mass and survival of females under lab conditions. We show through crosses and genomic and mRNA sequencing that curly-wing expression is associated with variation on a single autosome. In parallel analyses of flatwing, our results reinforce previous findings of X-linked single-locus inheritance. By combining insights into the genetic architecture of these alternative phenotypes with simulations and field observations, we show that the co-occurrence of these two adaptations impedes either from fixing, despite extreme fitness benefits, due to fitness epistasis. This co-occurrence of similar adaptive forms in the same populations might be more common than is generally considered and could be an important force inhibiting adaptive evolution in wild populations of sexually reproducing organisms.

Challenges and advances in measuring phenotypic convergence

Tests of phenotypic convergence can provide evidence of adaptive evolution, and the popularity of such studies has grown in recent years due to the development of novel, quantitative methods for identifying and measuring convergence. These methods include the commonly applied C1-C4 measures of Stayton (2015a), which measure morphological distances between lineages, and Ornstein-Uhlenbeck (OU) model-fitting analyses, which test whether lineages converged on shared adaptive peaks. We test the performance of C-measures and other convergence measures under various evolutionary scenarios and reveal a critical issue with C-measures: they often misidentify divergent lineages as convergent. We address this issue by developing novel convergence measures-Ct1-Ct4-measures-that calculate distances between lineages at specific points in time, minimizing the possibility of misidentifying divergent taxa as convergent. Ct-measures are most appropriate when focal lineages are of the same or similar geologic ages (e.g., extant taxa), meaning that the lineages' evolutionary histories include considerable overlap in time. Beyond C-measures, we find that all convergence measures are influenced by the position of focal taxa in phenotypic space, with morphological outliers often statistically more likely to be measured as strongly convergent. Further, we mimic scenarios in which researchers assess convergence using OU models with a priori regime assignments (e.g., classifying taxa by ecological traits) and find that multiple-regime OU models with phenotypically divergent lineages assigned to a shared selective regime often outperform simpler models. This highlights that model support for these multiple-regime OU models should not be assumed to always reflect convergence among focal lineages of a shared regime. Our new Ct1-Ct4-measures provide researchers with an improved comparative tool, but we emphasize that all available convergence measures are imperfect, and researchers should recognize the limitations of these methods and use multiple lines of evidence to test convergence hypotheses.

Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes

BACKGROUND

To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order.

RESULTS

We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group.

CONCLUSIONS

The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.

Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.

Genomics of hybrid parallel origin in Aquilegia ecalcarata

BACKGROUND

The parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear.

RESULTS

In this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata.

CONCLUSIONS

Our results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.

Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments

Regulating transcription allows organisms to respond to their environment, both within a single generation (plasticity) and across generations (adaptation). We examined transcriptional differences in gill tissues of fishes in the Poecilia mexicana species complex (family Poeciliidae), which have colonized toxic springs rich in hydrogen sulfide (H2S) in southern Mexico. There are gene expression differences between sulfidic and non-sulfidic populations, yet regulatory mechanisms mediating this gene expression variation remain poorly studied. We combined capped-small RNA sequencing (csRNA-seq), which captures actively transcribed (i.e. nascent) transcripts, and messenger RNA sequencing (mRNA-seq) to examine how variation in transcription, enhancer activity, and associated transcription factor binding sites may facilitate adaptation to extreme environments. csRNA-seq revealed thousands of differentially initiated transcripts between sulfidic and non-sulfidic populations, many of which are involved in H2S detoxification and response. Analyses of transcription factor binding sites in promoter and putative enhancer csRNA-seq peaks identified a suite of transcription factors likely involved in regulating H2S-specific shifts in gene expression, including several key transcription factors known to respond to hypoxia. Our findings uncover a complex interplay of regulatory processes that reflect the divergence of extremophile populations of P. mexicana from their non-sulfidic ancestors and suggest shared responses among evolutionarily independent lineages.

Selection leads to remarkable variability in the outcomes of hybridisation across replicate hybrid zones

Hybrid zones have been viewed as an opportunity to see speciation in action. When hybrid zones are replicated, it is assumed that if the same genetic incompatibilities are maintaining reproductive isolation across all instances of secondary contact, those incompatibilities should be identifiable by consistent patterns in the genome. In contrast, changes in allele frequencies due to genetic drift should be idiosyncratic for each hybrid zone. To test this assumption, we simulated 20 replicates of each of 12 hybrid zone scenarios with varied genetic incompatibilities, rates of migration, selection and different starting population size ratios of parental species. We found remarkable variability in the outcomes of hybridisation in replicate hybrid zones, particularly with Bateson-Dobzhansky-Muller incompatibilities and strong selection. We found substantial differences among replicates in the overall genomic composition of individuals, including admixture proportions, inter-specific ancestry complement and number of ancestry junctions. Additionally, we found substantial variation in genomic clines among replicates at focal loci, regardless of locus-specific selection. We conclude that processes other than selection are responsible for some consistent outcomes of hybridisation, whereas selection on incompatibilities can lead to genomically widespread and highly variable outcomes. We highlight the challenge of mapping between pattern and process in hybrid zones and call attention to how selection against incompatibilities will commonly lead to variable outcomes. We hope that this study informs future research on replicate hybrid zones and encourages further development of statistical techniques, theoretical models and exploration of additional axes of variation to understand reproductive isolation.

Convergent accelerated evolution of mammal-specific conserved non-coding elements in hibernators

Mammals maintain their body temperature, yet hibernators can temporarily lower their metabolic rate as an energy-saving strategy. It has been proposed that hibernators evolved independently from homeotherms, and it is possible that the convergent evolution of hibernation involved common genomic changes among hibernator-lineages. Since hibernation is a seasonal trait, the evolution of gene regulatory regions in response to changes in season may have been important for the acquisition of hibernation traits. High-frequency accumulation of mutations in conserved non-coding elements (CNEs) could, in principle, alter the expression of neighboring genes and thereby contribute to the acquisition of new traits. To address this possibility, we performed a comparative genomic analysis of mammals to identify accelerated CNEs commonly associated with hibernation. We found that accelerated CNEs are common to hibernator-lineages and could be involved with hibernation. We also found that common factors of genes that located near accelerated CNEs and are differentially expressed between normal and hibernation periods related to gene regulation and cell-fate determination. It suggests that the molecular mechanisms controlling hibernation have undergone convergent evolution. These results help broaden our understanding of the genetic adaptations that facilitated hibernation in mammals and may offer insights pertaining to stress responses and energy conservation.

Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes

Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide-rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide-rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide-adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both.

Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (i) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (ii) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected-and more pleiotropic-genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.

Similar enzymatic functions in distinct bioluminescence systems: evolutionary recruitment of sulfotransferases in ostracod light organs

Genes from ancient families are sometimes involved in the convergent evolutionary origins of similar traits, even across vast phylogenetic distances. Sulfotransferases are an ancient family of enzymes that transfer sulfate from a donor to a wide variety of substrates, including probable roles in some bioluminescence systems. Here, we demonstrate multiple sulfotransferases, highly expressed in light organs of the bioluminescent ostracod Vargula tsujii, transfer sulfate in vitro to the luciferin substrate, vargulin. We find luciferin sulfotransferases (LSTs) of ostracods are not orthologous to known LSTs of fireflies or sea pansies; animals with distinct and convergently evolved bioluminescence systems compared to ostracods. Therefore, distantly related sulfotransferases were independently recruited at least three times, leading to parallel evolution of luciferin metabolism in three highly diverged organisms. Reuse of homologous genes is surprising in these bioluminescence systems because the other components, including luciferins and luciferases, are completely distinct. Whether convergently evolved traits incorporate ancient genes with similar functions or instead use distinct, often newer, genes may be constrained by how many genetic solutions exist for a particular function. When fewer solutions exist, as in genetic sulfation of small molecules, evolution may be more constrained to use the same genes time and again.

Emx2 underlies the development and evolution of marsupial gliding membranes

Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.