Evolution Of Traits Research Articles

Evolution of gene regulatory networks in insects.

Evolution of gene regulatory networks in insects.

Unravelling fungal pathogenesis: Advances in CRISPR-Cas9 for understanding virulence and adaptation.

Unravelling fungal pathogenesis: Advances in CRISPR-Cas9 for understanding virulence and adaptation.

Phylogenomics reveals the slow-burning fuse of diatom evolution

Evolution is often uneven in its pace and outcomes, with long periods of stasis interrupted by abrupt increases in morphological and ecological disparity. With thousands of gene histories, phylogenomics can uncover the genomic signatures of these broad macroevolutionary trends. Diatoms are a species-rich lineage of microeukaryotes that contribute greatly to the global cycling of carbon, oxygen, and silica, which they use to build elaborately structured cell walls. We combined fossil information with newly sequenced transcriptomes from 181 diverse diatom species to reconstruct the pattern, timing, and genomic context of major evolutionary transitions. Diatoms originated 270 Mya, and after >100 My of relative stasis in morphology and ecology, a radiation near the Jurassic-Cretaceous boundary led to the diversity of habitats and cell wall architectures characteristic of modern diatoms. This transition was marked by a genome duplication and high levels of gene tree discordance. However, short generation times increase the probability of coalescence between speciation events, minimizing the impacts of incomplete lineage sorting and implicating sequence saturation and gene tree error as the main sources of discordance. Nevertheless, a rigorous tree-based approach to ortholog selection resulted in strongly supported relationships, including some that were uncertain previously. Three pulses of accelerated speciation were detected, two of which were associated with the evolution of novel traits and ecological transitions. The first 100 My of diatom evolution was a slow-burning fuse that led to a burst of innovations in ecology, morphology, and life history that are hallmarks of contemporary diatom assemblages.

Tempo and mode of evolution across multiple traits in an adaptive radiation of birds (Vangidae).

An ongoing challenge in macroevolutionary research is identifying common drivers of diversification amid the complex interplay of many potentially relevant traits, ecological contexts, and intrinsic characteristics of clades. In this study, we used geometric morphometric and phylogenetic comparative methods to evaluate the tempo and mode of morphological evolution in an adaptive radiation of Malagasy birds, the vangas, and their mainland relatives (Aves: Vangidae). The Malagasy radiation is more diverse in both skull and foot shape. However, rather than following the classic "early burst" of diversification, trait evolution accelerated well after their arrival in Madagascar, likely driven by the evolution of new modes of foraging and especially of a few species with highly divergent morphologies. Anatomical regions showed differing evolutionary patterns, and the presence of morphological outliers impacted the results of some analyses, particularly of trait integration and modularity. Our results demonstrate that the adaptive radiation of Malagasy vangas has evolved exceptional ecomorphological diversity along multiple, independent trait axes, mainly driven by a late expansion in niche space due to key innovations. Our findings highlight the evolution of extreme forms as an overlooked feature of adaptive radiation warranting further study.

Global asymptotic stability and bifurcation of an evolutionary Beverton-Holt model

We investigate an autonomous evolutionary extension of the classical discrete Beverton-Holt population model for a single species by integrating trait evolution through Evolutionary Game Theory. The resulting two-dimensional discrete system couples population density with trait dynamics, capturing the interplay between inherent growth rates and competitive interactions influenced by phenotypic traits. Utilizing a change of variables to simplify the analysis, we systematically classify the local and global stability of the system's equilibria. Our analysis reveals that the extinction equilibrium is globally asymptotically stable when the inherent growth rate parameter b 0 ≤ 1 becomes unstable otherwise. For b 0 > 1 , a unique interior fixed point emerges, which undergoes a Neimark-Sacker bifurcation, indicating the presence of invariant closed curves and potentially complex dynamics. We further delineate the global dynamics based on the evolution speed parameter σ 2 , employing techniques such as injectivity on absorbing regions and exploiting the system's mixed-monotone properties. Specifically, for 0 < σ 2 < 1 , we establish global stability by analyzing the dynamics around isoclines, while for 1 < σ 2 < 2 , the mixed-monotone nature of the mapping allows us to derive stability results for specific parameter subsets. This study extends the classical Beverton-Holt framework by incorporating evolutionary processes, providing deeper insights into how trait evolution can influence population dynamics and stability.

Appearance of transient heteromorphic large chromosome in glyphosate-resistant Amaranthus tuberculatus.

Glyphosate resistance in crop weeds is commonly attributed to rapid evolution through the amplification of the target gene, EPSPS (5-enolpyruvylshikimate-3-phosphate synthase). This amplification typically occurs through mechanisms such as unequal recombination, segmental duplications within the target chromosome, or the formation of ring chromosomes and extrachromosomal circular (ecc) DNA elements containing EPSPS. However, structural abnormalities in chromosomes not directly associated with EPSPS amplification have not been documented in the glyphosate-resistant weed population. Here, we describe the presence of a large chromosome found exclusively in the glyphosate-resistantAmaranthus tuberculatus (waterhemp) population but absent in susceptible counterparts. This large chromosome (~ 6μm) is approximately twice the size of normal chromosomes (~ 2-3μm) and is present in both male and female euploid plants (2n = 32) in a heteromorphic state. It aroses through pericentromeric heterochromatin expansion and duplications of the 5S rDNA locus but notably lacks the EPSPS gene. The large chromosome pairs with its normal homolog but was not transmitted to progeny in controlled greenhouse matings, suggesting a fitness cost in the absence of glyphosate selection pressure. This large chromosome offers a potential resource for the investigation of chromosome evolution of adaptive traits for glyphosate resistance in A. tuberculatus.

Relatedness, trait evolution, and climatic niche divergence in mammalian island endemics

Island mammals have influenced ecological and evolutionary theory since Darwin, and many of them provide textbook examples of the dramatic morphological evolution that often occurs in island communities. However, patterns of evolution in the climatic niches of island mammals have yet to be fully explored. Several hypotheses explaining niche divergence in island species have been introduced, linking niche evolution to increased competition among closely related or sympatric species, and as a by‐product of morphological evolution or geographical patterns. Here, we evaluate these hypotheses using closely related species pairs (sister taxa). We characterized the climatic niches of island endemic species and their closest relatives and calculated two metrics of niche divergence between the species (niche overlap and centroid distance). We compared these metrics between island endemics that have island‐dwelling sister taxa and those that have mainland‐dwelling sister taxa. We then related the degree of niche divergence to phylogenetic relatedness between the sister taxa, sympatry, morphological trait differences and island characteristics (isolation, size, age). Overall, despite significant niche divergence across species pairs, we found little evidence that competition or biotic interactions drive large‐scale climatic niche evolution in island mammals. Niche divergence in island‐endemic mammals is not driven by sympatry with their closest relatives, nor is it linked to phylogenetic relatedness. Furthermore, the phenotypic evolution of island‐endemic species does not lead to corresponding evolution in climatic niches. Instead, abiotic, geographical patterns appear to drive niche divergence in these species. Sister taxa that were more geographically isolated from each other had significantly lower niche overlaps. Island‐endemic mammals that live in montane regions likewise diverged from their closest relatives. These results suggest that competition between related species on islands may lead to niche partitioning only on local scales and that niche evolution in island‐endemic mammals may occur primarily in response to geographical patterns.

Unravelling the Effects of Ecology and Evolutionary History in the Phenotypic Convergence of Fishes.

Understanding the ecological drivers and limitations of adaptive convergence is a fundamental challenge. Here, we explore how adaptive convergence of planktivorous fishes has been influenced by multiple ecological factors, evolutionary history, and chance. Using ecomorphological data for over 1600 marine species, we integrate pattern-based metrics of convergence with evolutionary model fitting to test whether phenotypic similarities among specialist planktivores exceed expectations under null models and whether ecology, evolutionary history, or their combined effects best explain trait evolution. We find that planktivores are significantly more similar in phenotype than expected. Traits with functional relevance for prey detection and capture, such as eye diameter and lower jaw length, are strongly convergent, while general body size and shape are constrained by deep divisions between clades where the effects of evolutionary history are most pronounced. Since not all traits undergo strong selection toward a convergent ecomorph, their evolutionary trajectories have not entirely overcome ancestral differences in the multivariate trait space, resulting in a specific form of convergence termed conservatism. We show how adaptive responses to feeding ecology intertwine with other ecological pressures (i.e., light environment) and historical contingency to shape fish phenotype evolution over deep time, offering key insights into the generality of phenotypic evolution.

The role of insularity: Plants have few ornithophilous traits but are visited by morphologically more distinct hummingbirds in the Caribbean islands

Abstract Functional traits determine interactions between plants and pollinators, and to increase pollination efficiency, many plants have evolved traits to attract specific pollinator groups. However, biogeographical setting may influence trait evolution and biotic interactions. For instance, plants pollinated by hummingbirds often have ornithophilous traits, that is, flowers with elongated corollas, dilute nectar and red colours, but—due to colonization history, depauperate biotas and unstable environmental conditions—it might be disadvantageous for species to rely on mutualistic partners with specific functional traits on oceanic islands. Hummingbird‐visited plants on islands are thus expected to have fewer ornithophilous traits and be functionally less diverse in their interactions with hummingbirds. We compiled an extensive dataset of plant—hummingbird interactions (1030 plant and 181 hummingbird species) and associated functional traits. We divided the data into four biogeographical regions across the American mainland and the Caribbean islands and then tested whether biogeographical regions differed in the proportion of ornithophilous floral traits and functional diversity of plant—hummingbird interactions. We found that hummingbird‐visited plant communities of the Caribbean islands displayed the lowest proportion of traits typically associated with a functional adaptation towards bird‐mediated pollination, with on average the shortest corollas, the highest nectar concentrations and the largest proportion of non‐ornithophilous colours. Contrary to our expectations, plants in the Caribbean interacted with hummingbirds that were morphologically more distinct than the plants of mainland regions. Overall, we document a strong imprint of insularity on floral traits and interactions with hummingbirds. While hummingbird‐visited plants in the Caribbean displayed floral traits that support island theory, predicting less specific pollination systems on oceanic islands, the functional diversity of plant–hummingbird interactions in the Caribbean communities was higher than on the mainland, possibly driven by competition over resources. These results highlight the influence of insularity on functional traits and plant–pollinator interactions. Read the free Plain Language Summary for this article on the Journal blog.

Neutral transcriptome rewiring promotes quantitative disease resistance evolvability at the species level.

Quantitative disease resistance (QDR) is an immune response limiting pathogen damage in plants. It involves transcriptomic reprogramming of numerous genes, each having a small contribution to plant immunity. Despite the broad-spectrum nature of QDR, the evolution of its underlying transcriptome reprogramming remains largely uncharacterized. Here, we analyzed global gene expression in response to the necrotrophic fungus Sclerotinia sclerotiorum in 23 Arabidopsis (Arabidopsis thaliana) accessions of diverse origin and contrasting QDR phenotypes. Over half of the species pan-transcriptome displayed local responses to S. sclerotiorum, with global reprogramming patterns incongruent with accession phylogeny. Due to frequent small-amplitude variations, only ∼11% of responsive genes were common across all accessions, defining a core transcriptome enriched in highly-responsive genes. Co-expression and correlation analyses showed that QDR phenotypes result from the integration of the expression of numerous genes. Promoter sequence comparisons revealed that variation in DNA-binding sites within cis-regulatory regions contributes to gene expression rewiring. Finally, transcriptome-phenotype maps revealed abundant neutral networks connecting diverse QDR transcriptomes with no loss of resistance, hallmarks of robust and evolvable traits. This navigability associated with regulatory variation in core genes highlights their role in QDR evolvability. This work provides insights into the evolution of complex immune responses, informing models for plant disease dynamics.

Sexual selection and population spatial structure interact to shape sex-specific evolutionary responses in physiology.

Different selection pressures acting on females and males arising from sexual selection and sexual conflict may lead to sex-specific phenotypic expression of physiological traits. Importantly, sexual selection is affected by ecological and demographic factors. We explored whether population spatial structure modulates the effect of sexual selection on male and female standard metabolic rates and oxidative stress. For this purpose, we used selection lines of the seed beetle Callosobruchus maculatus subjected to divergent evolutionary regimes in the intensity of sexual selection (high vs. low, in polygamous vs. enforced monogamous populations, respectively) and the presence of metapopulation structure (absent vs. present). We found that the evolutionary treatments impacted physiological traits in a complex way. While in the selection regimes simulating metapopulation structure (i.e., divided populations) both sexes had similar metabolic rates, in undivided (unstructured) populations males had lower rates than females. Males from polygamous and undivided populations showed the lowest levels of antioxidant enzymes quantified as SOD, resulting in strong sexual dimorphism in SOD levels in this selection regime. The oxidative damage to lipids measured as TBARS levels, instead, were highest for both males and females from monogamous and undivided populations. On the whole, our results reveal two key insights. First, physiological traits evolve differently in females and males in response to sexual selection intensity and population spatial structure. Second, such sex-specific physiological responses are linked to selective pressures acting mostly on males. We highlight the importance of considering ecological and demographic factors when evaluating whether sexual selection drives sex-specific trait evolution.

Mitochondrial Genomes of the Robberflies Clephydroneura jiangxiensis and Maira xizangensis (Diptera: Asilidae) and Phylogeny of Three Superfamilies.

Asilomorpha, an infraorder of predatory Diptera (Brachycera), is of significant evolutionary interest due to their remarkable ecological diversity, broad size range, and specialized feeding behaviors. However, phylogenetic studies of this group have been limited by sampling challenges. In this study, we sequenced the complete mitochondrial genomes of two Chinese endemic species, Clephydroneura jiangxiensis (C. jiangxiensis) and Maira xizangensis (M. xizangensis), using whole-genome random sequencing. By integrating these novel data with published sequences from NCBI, we reconstructed the phylogeny of three superfamilies (Asiloidea, Empidoidea, and Nemestrinoidea). Both mitochondrial genomes exhibit the typical 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and display pronounced AT bias. Congruent results from maximum likelihood analysis and Bayesian inference strongly supported the ideas that both new species are placed in Asilidae and that the Asilidae family is monophyletic. However, relationships among the three superfamilies remain unclear. Our results suggest that (1) although Asiloidea and Nemestrinidea are closely related, the potential positioning of Nemestrinoidea as an independent superfamily is worth investigating; and (2) Empidoidea may form a sister group to Asiloidea + Nemestrinidae, though this hypothesis requires further corroboration given the basal position of Hemipenthes hebeiensis (Bombyliidae). These findings highlight the need for expanded taxon sampling, particularly of underrepresented families, to resolve deep-level relationships within Asilomorpha. Clarifying the phylogenetic relationships within Asilomorpha will facilitate future investigations into their evolutionary origins and the evolution of characteristic traits.

The complete mitochondrial genome of Sinojackia microcarpa: evolutionary insights and gene transfer

BackgroundAs a dicotyledonous plant within the Styracaceae family, Sinojackia microcarpa (S. microcarpa) is notable for its library-shaped fruit and sparse distribution, serving as a model system for studying the entire tree family. However, the scarcity of genomic data, particularly concerning the mitochondrial and nuclear sequences of S. microcarpa, has substantially impeded our understanding of its evolutionary traits and fundamental biological mechanisms.ResultsThis study presents the first complete mitochondrial genome sequence of S. microcarpa and conducts a comparative analysis of its protein-encoding genes across eight plant species. Our analysis revealed that the mitochondrial genome of S. microcarpa spans 687,378 base pairs and contains a total of 59 genes, which include 37 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Sixteen plastid-derived fragments strongly linked with mitochondrial genes, including one intact plastid-related gene (rps7), were identified. Additionally, Ka/Ks ratio analysis revealed that most mitochondrial genes are under purifying selection, with a few genes, such as nad9 and ccmB, showing signs of relaxed or adaptive evolution. An analysis of twenty-nine protein-coding genes from twenty-four plant species reveals that S. microcarpa exhibits a closer evolutionary relationship with species belonging to the genus Camellia. The findings of this study provide new genomic data that enhance our understanding of S. microcarpa, and reveal its mitochondrial genome’s evolutionary proximity to other dicotyledonous species.ConclusionsOverall, this research enhances our understanding of the evolutionary and comparative genomics of S. microcarpa and other plants in the Styracaceae family and lays the foundation for future genetic studies and evolutionary analyses in the Styracaceae family.

Bioenergetics and the Evolution of Cellular Traits.

Evolutionary processes have transformed simple cellular life into a great diversity of forms, ranging from the ubiquitous eukaryotic cell design to the more specific cellular forms of spirochetes, cyanobacteria, ciliates, heliozoans, amoeba, and many others. The cellular traits that constitute these forms require an evolutionary explanation. Ultimately, the persistence of a cellular trait depends on its net contribution to fitness, a quantitative measure. Independent of any positive effects, a cellular trait exhibits a baseline energetic cost that needs to be accounted for when quantitatively examining its net fitness effect. Here, we explore how the energetic burden introduced by a cellular trait quantitatively affects cellular fitness, describe methods for determining cell energy budgets, summarize the costs of cellular traits across the tree of life, and examine how the fitness impacts of these energetic costs compare to other evolutionary forces and trait benefits.

CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution.

Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analysing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development.

Identification of genetic signatures of positive selection in apes linked to life-history trait adaptations.

Apes, including humans, exhibit distinctive life history traits such as increased brain mass, delayed sexual maturity, and extended longevity compared to non-ape primates. These pronounced interspecific differences likely arise from underlying genetic architecture. However, the molecular mechanisms contributing to these traits remain largely unknown. This study aims to identify genetic factors under positive selection that may have contributed to the evolution of ape-specific life history traits, particularly extended longevity. Comparative genomic analyses were performed between 7 ape species and 22 non-ape primate taxa to identify positively selected genes (PSGs). Functional enrichment analyses were conducted to determine the biological processes associated with these PSGs. Additionally, expression analyses were carried out to assess tissue-specific patterns and their potential roles in neurodevelopment and systemic homeostasis. A total of 143 PSGs were idetntified, showing significant enrichment in biological processes including homeostatic regulation, protein complex assembly, and G protein-coupled receptor signaling pathways. Among these, ADCY5, PRKCB, and IL2 were of particular interest due to their established roles in longevity-associated mechanisms. Expression analyses revealed tissue-specific patterns suggesting potential involvement in brain evolution, neurodevelopment, and glucose homeostasis. This study provides molecular insights into the genetic mechanisms underlying longevity in apes and highlights key biological processes that may have contributed to the evolution of ape-specific life history traits. These findings enhance our understanding of how positive selection has shaped complex phenotypes, particularly extended lifespan, in the ape lineage.

Origins and diversity of invasive brushtail possums (Trichosurus vulpecula) in New Zealand surveyed with mtDNA haplotype and nuclear microsatellite data

ABSTRACT The brushtail possum Trichosurus vulpecula is native to Australia where six subspecies exist in distinct regions. A composite invasive population is established in Aotearoa New Zealand, which has since been subject to localised bouts of culling. We surveyed population genetic structure across New Zealand to identify the scale of genetic diversity introduced to New Zealand and the resulting pattern of admixture. Australian brushtail possums have high mitochondrial diversity (17%) and prominent spatial structure. Thirty-eight haplotypes among 25 New Zealand population samples (n = 465) were closely related to 45 haplotypes sampled from Victoria and Tasmania in Australia (n = 120), but just one was shared. High haplotype diversity is consistent with multiple successful introductions and rapid population expansion in New Zealand. Nuclear diversity of microsatellite loci screened in 18 New Zealand population samples (n = 374) comprised five genotypic clusters (K = 5), but these groups did not correlate with geography. An overall signal of genetic partitioning within the invasive population suggests limited mixing but ongoing management towards eradication will influence patterns of population recovery, migration and evolution of traits including toxin resistance. We consider the implications of mixed ancestry of the invasive population in terms of variation in toxin tolerance detected in New Zealand.

Global key areas for anuran tadpole discovery

Abstract Anurans are the most threatened group of tetrapods. Although the number of Data Deficient species has been drastically reduced during the latest global assessment, there remain crucial gaps in knowledge about their biology. For more than half of all species, their larval stages are entirely unknown, posing a major obstacle to effective conservation. This is especially important for species with a biphasic life cycle, in which drivers of extinction can impact tadpoles and adults differently. To address this, we integrated global data on anuran tadpoles with ancestral state reconstructions and Geographic Information System based analyses to identify key areas for discovering free-living tadpoles. Our results show that strategically focusing research on 0.25% of Earth’s terrestrial surface could reveal more than half of the undescribed tadpoles, and covering 1% could account for all of them. These priority areas are concentrated mainly in biodiversity hotspots and include the Tropical Andes, Eastern Brazil, Tropical Africa, India, Southeast Asia and New Guinea. Each region exhibits unique ecological and evolutionary traits in anuran larval diversity, highlighting their importance for targeted research. Given the alarming rate of habitat loss and the high biodiversity within these regions, this study underscores the need for urgent conservation efforts to protect both known diversity and diversity yet to be discovered.

Cytogenetic insights into Sosippinae (Araneae, Lycosidae) reveal pronounced diploid number reduction in Aglaoctenus and elevated number of rDNA loci in two unrelated species.

Cytogenetic insights into Sosippinae (Araneae, Lycosidae) reveal pronounced diploid number reduction in Aglaoctenus and elevated number of rDNA loci in two unrelated species.

Complete metamorphosis promotes morphological and functional diversity in Caudata

Abstract Metamorphosis, a common and spectacular developmental process, involves major phenotypic changes often linked to environmental transitions. Understanding how these changes affect morphological evolution is crucial for examining metamorphosis's evolutionary impacts. In this study, we analysed the role of metamorphosis and life cycle variation on the morphological evolution of the mandible in Caudata (salamanders and newts), a clade that exhibits a great diversity of life cycles and ecologies. We focused on the mandible, a key component of the masticatory apparatus, to investigate how life cycle variation may influence the diversification of feeding modes. Using 3D geometric morphometrics on 317 extant species of Caudata, we found that both life cycle and size influence mandible shape, with complex interactions between these factors. The morphology of the mandibular bones evolved more independently in species undergoing complete metamorphosis compared to those with partial metamorphosis, likely facilitating feeding diversification in terrestrial adults. On the other hand, high morphological integration in species undergoing partial metamorphosis could promote the rapid evolution of traits, resulting in the differentiation of more disparate morphologies, potentially aiding paedomorphic species in adapting to challenging environments. This study highlights the interplay between metamorphosis and the environment in shaping morphological evolution among species and provides new insights into the role of heterochrony in the morphological diversification of organisms. Read the free Plain Language Summary for this article on the Journal blog.