Biology subjects

Elias, M.

Publications and source records attributed to Elias, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Decoupled wing evolution reveals trait-specific links between morphology, geography, and diversification in Ithomiini butterflies.

Understanding when species diversification and phenotypic evolution are coupled remains a central challenge in macroevolution. Such coupling may depend on the traits considered, phenotypic integration, or the geographic context in which diversification occurs. Here, we investigate these relationships in Ithomiini, a diverse Neotropical butterfly tribe whose diversification is strongly associated with the Andes-Amazonia system. We quantified forewing and hindwing size and shape for 1,618 individuals representing 291 species using geometric morphometrics, and combined these data with phylogenetic comparative methods, diversification-rate estimates, and spatial analyses of species distributions. Evolutionary rate shifts were largely trait- and wing-specific, indicating limited coupling between forewing and hindwing evolution. Across the phylogeny, wing size evolution and extant wing size were not associated with species diversification, nor was hindwing shape evolution. By contrast, forewing shape evolutionary rates showed a positive association with diversification. Spatial analyses revealed that this coupling was geographically concentrated in the Andes, where high diversification rates coincided with elevated forewing size and shape diversity and increased forewing evolutionary rates. Hindwing diversity, by contrast, more closely tracked phylogenetic diversity and showed weaker or opposing relationships with diversification. Our results show that diversification and phenotypic evolution in Ithomiini are neither generally coupled nor fully independent, but linked in trait-specific and geographically structured ways. More broadly, they highlight the need to decompose complex phenotypes and integrate spatial context when testing macroevolutionary coupling.

ecology↗

bioRxiv2026

Do tropical birds avoid evasive prey? An experimental study in Ecuadorian avian communities

The effect of predator behaviours on the evolution of colour pattern has been extensively studied in chemically defended prey but much less so in evasive prey, although similar selection regimes might be at play. Most previous work on the recognition and learning of colour patterns by predators has relied on experiments with few model predator species, preventing a proper assessment of how natural predator communities shape the evolution of prey signals. Here, we investigate predation on evasive iridescent blue Morpho helenor butterflies by wild avian communities in a tropical forest, using artificial butterflies exposed to natural bird assemblages attracted to insect-light traps in the field. We presented five prey types: evasive (local and exotic Morpho), cryptic, palatable-control and unpalatable-control. We recorded attacks from 43 different bird species, and compared attack latency, attack order and predation exerted by different birds on different prey types. Most birds avoided evasive and defended prey, but attack responses differed depending on their levels of specialization towards insect prey. Avoidance of conspicuous coloured prey was more prevalent in specialist flight-feeding, invertivorous birds, whereas more opportunistic treehunter and frugivorous guilds had weaker discrimination. Exotic and local evasive iridescent blue Morphos experienced similar predation rates, suggesting a generalization of iridescent blue signals associated with evasiveness by most birds. Finally, contrasting selection on ventral vs. dorsal patterns was detected in M. helenor, where cryptic ventral surfaces were exposed to attack by ground-foraging birds, whereas conspicuous iridescent blue coloration displayed during flight is associated with reduced attack rates. By revealing potential differences in the responses of specialist and generalist predators, this study highlights the importance of accounting for diversity of predator traits and behaviours when investigating the evolution of aposematism, mimicry, and other anti-predator adaptations.

evolutionary biology↗

bioRxiv2026

The colourless dictyochophyte Ciliophrys sp. Baltic secondarily lacks a plastid but hosts a bacterial endosymbiont

The loss of an organelle represents an extreme case of reductive evolution. Only a few plastid loss events have been documented and they seem to be particularly rare in free-living ancestrally photosynthetic taxa. We isolated a new phagotrophic protist, Ciliophrys sp. Baltic, representing a poorly studied non-photosynthetic lineage in the stramenopile algal class Dictyochophyceae. Genomic and transcriptomic data from this organism demonstrate that it lacks a plastid genome and nuclear genes critical for plastid biogenesis. The plastid organelle is thus most likely secondarily missing from Ciliophrys sp. Baltic, although a few enzymes originally targeted to the plastid persist with a changed localization. Unexpectedly, Ciliophrys sp. Baltic harbors a bacterial endosymbiont, Candidatus Penulousia baltica sp. nov. (Rickettsiales). Analysis of its complete genome sequence uncovered unique aspects of its metabolism not previously reported in other Rickettsiales. The bacterium exploits its host metabolically and presumably manipulates it with an arsenal of putative effector proteins. However, we also found that it might help offset some of the biosynthetic deficiencies of its host stemming from the plastid loss by providing haem and a lysine precursor. Altogether, our study establishes a new single-cell model system for studying plastid loss and endosymbiont acquisition.

evolutionary biology↗

bioRxiv2026

Charting the landscape of organellar genome evolution in eustigmatophyte algae

Organellar genomes are both a resource for reconstructing organismal phylogenies and interesting subjects for evolutionary studies. Herein, we focused on the organellar genomes of eustigmatophytes (eustigs), a class of the algal phylum Ochrophyta with a growing biotechnological potential, and massively expanded the existing limited sample by 51 new organellar genomes. Analyses of this large dataset provided a robustly resolved eustig phylogeny and important insights into the evolution of unique features of eustig organellar genomes. Eustig plastomes are rather stable in terms of the gene content, with only minor differences stemming from differential gene loss and rare lineage-specific gain. In contrast, eustig mitogenomes contain a very stable core of conserved genes accompanied by a broadly varying shell comprising "accessory" genes. Notably, the new data illuminated the origin of two mitochondrial genes previously deemed eustig-specific, namely orfX and orfY that were found to have evolved, respectively, by rps4 duplication and extreme divergence of an rps1 ortholog. Most interestingly, we identified five previously unrecognized orthogroups of mysterious mitochondrial orfs that are patchily distributed across eustigs yet likely evolved in the ancestor of this class. These orfs have no discernible homologs outside eustigmatophytes but are predicted to encode multipass membrane proteins with a soluble C-terminal domain. Our results also revise some of the previous conclusions regarding the mitochondrial translation in eustigs and suggest the recruitment of a group of unusual tRNAs for a translation-independent function in the genus Vischeria. Our study thus provides a glimpse into a "dark matter" of mitochondrial biology in eustigmatophytes. Significance statementOrganellar genomes have been characterized for only a small subset of members of Eustigmatophyceae, a class of biotechnologically attractive coccoid microalgae within the phylum Ochrophyta. In this study, we present >50 newly determined organellar genome sequences from diverse eustigmatophytes, filling most major gaps in sampling across the eustigmatophyte phylogenetic tree and more than doubling the number of species represented. This greatly expanded dataset was analyzed to provide numerous new insights into phylogenetic relationships within the class, variation in organellar gene content, and the evolutionary processes and trends shaping eustigmatophyte organellar genomes. Most notably, our work reveals a surprisingly rich and evolutionarily dynamic repertoire of eustigmatophyte-specific mitochondrial genes, pointing to a functional "dark matter" within eustigmatophyte mitochondria.

evolutionary biology↗

bioRxiv2026

Repeated trends in altitudinal gradients of diversity: how habitat filtering and biotic interactions structure ecological communities

Understanding how biodiversity is structured along tropical elevational gradients requires disentangling the relative roles of regional evolutionary history and local processes shaping ecological assemblies. Here, Ithomiini butterfly communities were studied along repeated elevational gradients in two Neotropical regions with contrasting evolutionary histories: the Amazonian Andes and the Guiana Shield. The study tested whether similar elevational patterns of taxonomic, mimetic, and phylogenetic structure emerge despite distinct regional species pools, and whether abiotic and biotic factors contribute to shaping these patterns. Despite marked regional differences in overall richness, consistent elevational patterns emerged across both regions. Taxonomic and mimetic richness increased with elevation and were accompanied by stronger phylogenetic clustering, indicating that similar habitat filtering processes operate along altitudinal gradients irrespective of regional context. Phylogenetic {beta}-diversity was predominantly driven by lineage turnover, particularly in the Andes, highlighting the role of elevational gradients in promoting replacement of phylogenetically distinct lineages rather than simple species loss. These shared patterns suggest that altitude has a strong and repeatable effect on community structure, with habitat filtering acting locally on regionally distinct species pool. Abiotic factors such as temperature appeared to constrain species distributions at broad spatial scales, whereas biotic interactions acted more locally. In particular, butterfly diversity was positively associated with potential host plant richness and predation pressure, indicating that ecological interactions can further shape local community composition once broad-scale environmental constraints are accounted for. By integrating phylogenetic structure, biotic interactions, and environmental gradients across regions with contrasting evolutionary histories, this study shows how regional species pools and local ecological filtering jointly shape tropical biodiversity and highlights that similar elevational assembly processes could arise independently across the Neotropics.

ecology↗

bioRxiv2025

Phylogeny, systematics and evolution of mimicry patterns in Neotropical limenitidine butterflies

The Neotropical butterfly genus Adelpha Hubner exhibits remarkable species diversity and striking convergence in wing colour patterns potentially explained by mimicry, making it an exceptional model for exploring trait evolution and its relationship with speciation. To date, unresolved phylogenetic relationships hinder a comprehensive understanding of the evolutionary biology of the genus. Using a novel multi-marker dataset combining one mitochondrial and 15 nuclear gene fragments, we generate the most comprehensive phylogeny of the genus Adelpha to revisit its systematics and investigate the evolution of mimicry colour patterns. Our data set encompasses 83 of the 87 known extant species and six Limenitis species that were recently excluded from Adelpha (134 of c. 160 subspecies in total), collectively displaying 14 distinct mimicry patterns. We provide conclusive evidence that corroborates previous work on the polyphyly of Adelpha as historically conceived, and describe the genus Adelphina Paez & Willmott n. gen. to stabilize the nomenclature, both genera representing Neotropical limenitidines. The comprehensive phylogeny provided in this study lays a solid foundation for future research into the processes driving diversification within these species interacting through mimicry. Ancestral character state reconstruction reveals gradual evolution of mimicry pattern. The more common mimicry pattern IPHICLUS (forewing with orange subapical spot and white band) is inferred as ancestral, but repeated convergent evolution is also recovered. Evolutionary convergence is also observed for the second most abundant mimicry pattern, COCALA (orange-white banded). Increased rates of mimicry pattern evolution are also found toward the equator. These results underscore the complexity of mimicry evolution in the Neotropical limenitidines i.e., Adelpha and Adelphina, emphasizing the need to explore its interplay with other biotic and abiotic factors.

evolutionary biology↗

bioRxiv2025

Genetic parallelism underpins convergent mimicry coloration across Lepidoptera

Convergent evolution, the repeated evolution of similar phenotypes in response to the same selective pressures across multiple lineages, is widespread in nature. The extent to which the same genetic mechanisms contribute to convergent evolution could reveal whether the pathway towards these optimal endpoints is flexible or constrained to follow a particular route. Although mimicry of aposematic colour patterns is well known in Lepidoptera, our knowledge of the genetic basis of these convergent patterns is mostly restricted to a few closely-related species. Here we study the genetic basis of mimicry across seven species of Ithomiini and Heliconius butterflies and a day-flying Chetone moth, representing lineages that diverged between [~]1-120 Mya, each presenting similar colour pattern switches. In all the butterfly species, the genetic variants most strongly associated with convergent colour pattern switches are similarly located in non-coding regions near the genes ivory and optix. Colour pattern variation in the moth is associated with a [~]1 Mb inversion around ivory paralleling the supergene architecture of the co-mimic Heliconius numata. In contrast to previous studies in Heliconius, there is limited evidence of alleles shared by means of hybridization in convergence among closely-related ithomiine species. Repeated parallel evolution of regulatory switches via reuse of the same two genes suggests that convergent colour pattern evolution is highly constrained, even across large evolutionary timescales.

evolutionary biology↗

bioRxiv2025

Perceptual maps reveal rampant convergence in butterfly wing patterns across the Neotropics

In 1879, Fritz Muller formulated the first mathematical evolutionary model to explain mutualistic mimicry between coexisting defended prey. Yet, whether local mimicry drives the structure of aposematic prey signals across their entire geographic distribution remains untested because the perception of pattern similarity has never been assessed at large spatial scale. Here, we implement a citizen science survey to map, throughout the Neotropics, variation in the wing patterns of heliconiine butterflies (Nymphalidae) as perceived by vertebrate cognitive systems. We show that despite a continuum of perceived similarity in wing patterns at the continental scale, the convergence of sympatric species into discrete mimicry rings is ubiquitous among local communities. These results expand Mullers historical predictions by quantifying the rampant convergence of prey signals across an entire continent.

evolutionary biology↗

bioRxiv2025

Müllerian mimicry in Neotropical butterflies: One mimicry ring to bring them all, and in the jungle bind them

Understanding the mechanisms underlying species distributions and coexistence is essential to predict and prevent the impacts of global change, particularly in biodiversity hotspots. However, the effects of biotic interactions may be challenging to investigate at large spatial scales. Leveraging well-characterized Mullerian mimetic systems in Neotropical butterflies, we investigated spatial patterns of mutualistic mimetic interactions within and between two tribes of aposematic Nymphalid butterflies: the Heliconiini (Heliconiinae) and the Ithomiini (Danainae). Despite 85 My of independent evolutionary histories, many species share similar warning wing patterns across the Neotropics. In this study we show that both tribes form similar biodiversity hotspots with a high prevalence of rare species and mimetic patterns in the tropical Andes. However, we reveal a higher relative richness of heliconiine butterflies than ithomiines in the Amazon basin contrasting with the Andean concentration of ithomiine diversity. Despite this difference in broadscale diversity patterns, we also document large-scale spatial associations among phenotypically similar species within and between tribes, thereby providing new empirical evidence for Fritz Mullers historical model of mutualistic mimicry at a continental scale. Furthermore, comparative phylogenetic analyses suggest that co-mimetic species within and between tribes have converged towards similar climatic niches as a response to selection favoring co-occurrence. Our findings illustrate the strength of mutualistic interactions in shaping biodiversity patterns at continental scale and in supporting niche convergence even across millions of years of evolution. Critically, it also emphasizes the pervasive vulnerability of mimetic communities, bound by positive interactions, to disassembly induced by climate change. Significance statementMullerian mimicry is a remarkable example of convergent evolution driven by natural selection where coexisting prey species converge in their warning signal advertising their defenses to predators. Heliconiine and ithomiine butterflies found throughout Neotropical rainforests were instrumental in Fritz Mullers historical model, which provided the mechanism for such resemblance. Leveraging decades of fieldwork and museum collections, we show that species with similar color patterns present strikingly similar spatial distributions, regardless of how closely related they are. Such co-occurrence appears reinforced by the evolution of similar climatic requirements among look-alike species. Our findings emphasize the key role of mutualistic interactions in shaping large-scale patterns of biodiversity and supporting convergence in the climatic niches of species spanning across phylogenetically distant clades.

evolutionary biology↗

bioRxiv2025

The core MICOS complex subunit Mic60 has been substituted by two cryptic mitofilin-containing proteins in Euglenozoa

Cristae enclose respiratory chain complexes, making them the bioenergetic subcompartments of mitochondria. The MICOS complex is among the inducers of membrane curvature needed for crista formation. Resembling the respiratory chain complexes, MICOS is organized around a core protein, the mitofilin-domain bearing Mic60, that was inherited from the alphaproteobacterial progenitor of mitochondria. Extant alphaproteobacteria express Mic60 to form their own bioenergetic subcompartments, demonstrating the permeance of Mic60s form and function during prokaryotic and eukaryotic evolution. Yet, unlike virtually all aerobic eukaryotes, Mic60 is not encoded within the genomes of the multifarious protists that comprise the phylum Euglenozoa, including trypanosomes. Here, we show that Mic60 has been replaced in euglenozoans by two cryptic mitofilin domain-containing MICOS subunits, Mic34 and Mic40. Contrasting alphaproteobacterial and mitochondrial Mic60, these are not integral membrane proteins. Mic34 and Mic40 are as diverged from each other as both are to canonical Mic60. Reverse genetics revealed they are intertwined with the oxidative protein folding pathway required for mitochondrial-and crista-biogenesis, veiling a potential membrane remodeling role. Nevertheless, Mic34 binds phospholipid bilayers in vitro. Mic34 and Mic40 heterologous expression remodels gammaproteobacterial cytoplasmic membranes, like Mic60. Unexpectedly, Mic34 overexpression elaborates the simplified tubular mitochondrion of a Trypanosoma brucei life cycle stage with repressed oxidative phosphorylation. Furthermore, this activity was ablated by mutations to Mic34s mitofilin domain that correspond to essential motifs found in yeast Mic60s mitofilin domain. Thus, the mitofilin protein family is more diverse than originally supposed, with two of its structurally most divergent members altering the core of euglenozoan MICOS.

molecular biology↗

bioRxiv2024

Quantifying the success of prey crypsis, aposematism and evasiveness in avoiding avian predators attack

Antipredator defences typically act at distinct stages of the predation sequence--encounter, identification, approach, and subjugation. However, their effectiveness has rarely been quantified and compared simultaneously in wild predator-prey systems. We conducted a study in Peru, where we installed aviaries at two localities and recorded the responses of wild avian predators to three types of antipredator defences--crypsis, aposematism, and evasiveness--expressed by three butterfly species. The study included both immature and adult birds from insectivorous species in forest and urban environments. We tested the theoretical expectations that cryptic butterflies (Nymphalidae: Euptychiina) were rarely detected, aposematic Heliconius (Nymphalidae: Heliconiinae) were often sighted but seldom attacked, and evasive Spicauda (Hesperiidae: Eudaminae) were frequently detected and attacked but evaded capture at higher rates. Despite these distinct defensive strategies, mortality rates among prey types were largely similar, but predator life stage strongly influenced defence effectiveness. Immature birds were more likely to attack Heliconius, possibly reflecting a lack of learned avoidance for aposematic signals. Additionally, predator family influenced predation patterns, with more skilled insectivores (e.g., Vireonidae) showing higher capture success against defended prey. These findings illuminate the evolutionary pressures that shape predator behaviour and prey defences in tropical ecosystems, where high predator diversity possibly maintains the coexistence of multiple defensive strategies. The observed similar mortality rates underscore the adaptive value of these defences, as they collectively distribute the total predation pressure across prey species.

ecology↗

bioRxiv2024

Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation

A major question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for addressing how new species arise because they still show key morphological and ecological adaptations associated with speciation. While most studied recent radiations have evolved in an insular environment, less research has been carried out on continental radiations with complex species interactions. Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini) have rapidly radiated in the Neotropics. They are classical models for Amazonian biogeography and colour pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus, and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, patterns of hybridisation and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridisation and putative hybrid species in both radiations, which may have facilitated their rapid diversification. Moreover, dozens of chromosomal fusions and fissions were identified between congeneric species, and even some within species. We conclude that interactions between geography, hybridisation and chromosomal rearrangements have contributed to these two rapid radiations in the highly diverse Neotropical region. We suggest that rapid radiations may be spurred by repeated periods of geographic isolation during Pleistocene climate oscillations, combined with lineage-specific rapid accumulation of incompatibilities during allopatric phases, followed by secondary contact with some gene exchange. Significance StatementUnderstanding factors contributing to rapid speciation is a key aim of evolutionary biology. Here we focus on two rapid radiations of Neotropical butterflies. Our genomic data with broad taxonomic and geographic coverage reveal rampant hybridisation and chromosomal rearrangements, each likely contributing to the high diversification rates. Our study highlights the use of genomic data to resolve taxonomically challenging species groups and elucidate drivers of diversification in rapid radiations. We show that for biodiversity hotspots with recent radiations, barcoding is insufficient to characterise species richness due to gene flow and recent speciation. The taxonomic implications of both introgression and karyotype diversity for species delimitation are important to consider during monitoring and management of biodiversity in these vulnerable habitats.

evolutionary biology↗

bioRxiv2024

Origin of the far-red absorbance in eustigmatophyte algae red-shifted Violaxanthin-Chlorophyll a Protein

Photosynthetic organisms harvest light for energy. Some eukaryotic algae have specialized in harvesting far-red light by tuning chlorophyll a absorption through a mechanism still to be elucidated. Here, we combined optically detected magnetic resonance and pulsed electron paramagnetic resonance measurements on red-adapted light-harvesting complexes, rVCP, isolated from the freshwater eustigmatophyte alga Trachydiscus minutus to identify the location of the pigments responsible for this remarkable adaptation. The pigments have been found to belong to an excitonic cluster of chlorophylls a at the core of the complex, close to the central carotenoids in L1/L2 sites. A pair of structural features of the Chl a403/a603 binding site, namely the histidine-to-asparagine substitution in the magnesium-ligation residue and the small size of the amino acid at the i-4 position, are proposed to be the origin of this trait. Phylogenetic analysis of various eukaryotic red antennae identified several potential LHCs that could share this tuning mechanism.

biophysics↗

bioRxiv2024

Phylogenomics defines Streptofilum as a novel deep branch of streptophyte algae

Streptophytes constitute a major organismal clade comprised of land plants (embryophytes) and several related green algal lineages. Their seemingly well-studied phylogenetic diversity was recently enriched by the discovery of Streptofilum capillaum, a simple filamentous alga forming a novel deep streptophyte lineage in a two-gene phylogeny1. A subsequent phylogenetic analysis of plastid genome-encoded proteins resolved Streptofilum as a sister group of nearly all known streptophytes, including Klebsormidiophyceae and Phragmoplastophyta (Charophyceae, Coleochaetophyceae, Zygnematophyceae, and embryophytes)2. In a stark contrast, another recent report, published in Current Biology by Bierenbroodspot et al.3, presented a phylogenetic analysis of 845 nuclear loci resolving S. capillatum as a member of Klebsormidiophyceae, nested among species of the genus Interfilum. Here we demonstrate that the latter result is an artefact stemming from an unrecognized contamination of the transcriptome assembly from S. capillatum by sequences from Interfilum paradoxum. When genuine S. capillatum sequences are employed in the analysis, the position of the alga in the nuclear genes-based tree fully agrees with the plastid genes-based phylogeny. The "intermediate" phylogenetic position of S. capillatum predicts it to possess a unique combination of derived and plesiomorphic traits, here exemplified, respectively, by the "Rho of plants" (ROP) signaling system and the cyanobacteria-derived plastidial transfer-messenger ribonucleoprotein complex (tmRNP). Our results underscore S. capillatum as a lineage pivotal for the understanding of the evolutionary genesis of streptophyte, and ultimately embryophyte, traits.

plant biology↗

bioRxiv2024

Arf family GTPases are present in Asgard archaea

The emergence of eukaryotes from their prokaryotic ancestors is one of the most fundamental evolutionary events in the history of life. Little is robustly known about how eukaryogenesis occurred, but a major breakthrough came with the identification of the Asgardarchaeota, the closest prokaryotic lineage to eukaryotes yet discovered. Endomembrane organelles, and the capacity to transport material between them, are major hallmarks of eukaryotic cells. The Arf family GTPases are crucial regulators of organelle dynamics in eukaryotes, functioning in vesicle budding, membrane tethering and membrane-cytoskeleton interactions. Although an expanded GTPase complement has been reported in the Asgardarchaeota, the specific origins of the Arf family remain elusive. Here we report a new group of prokaryotic GTPases, the ArfRs. Widely present in Asgardarchaeota and almost exclusive to them, it is the clade from which all eukaryotic Arf family proteins are derived. Heterologous expression of representative Asgardarchaeota ArfR proteins in the model eukaryote Saccharomyces cerevisiae and X-ray crystallographic studies demonstrate that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results show that Arf family GTPases are present in Asgardarchaeota, and strongly suggest that they originated in the archaeal contributor to eukaryogenesis, providing support for nascent endomembrane system capacity evolving early in eukaryogenesis.

evolutionary biology↗

bioRxiv2024

Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics

Ochrophyta is a vast and morphologically diverse group of algae with complex plastids, including familiar taxa with fundamental ecological importance (diatoms or kelp), and a wealth of lesser-known and obscure organisms. The sheer diversity of ochrophytes poses a challenge for reconstructing their phylogeny, with major gaps in sampling and an unsettled placement of particular taxa yet to be tackled. We sequenced transcriptomes from 25 strategically selected representatives and used these data to build the most taxonomically comprehensive ochrophyte-centered phylogenomic supermatrix to date. We employed a combination of approaches to reconstruct and critically evaluate the relationships among ochrophytes. While generally congruent with previous analyses, the updated ochrophyte phylogenomic tree resolved the position of several taxa with previously uncertain placement, and supported a redefinition of the class Synchromophyceae. Our results indicated that the heterotrophic plastid-lacking heliozoan Actinophrys sol is not a sister lineage of ochrophytes, as proposed recently, but rather phylogenetically nested among them. In addition, we found Picophagus flagellatus to be a secondarily heterotrophic ochrophyte lacking all hallmark plastid genes, yet exhibiting mitochondrial proteins that seem to be genetic footprints of lost plastid organelle. We thus document, for the first time, plastid loss in two separate ochrophyte lineages. Altogether, our study provides a new framework for reconstructing trait evolution in ochrophytes and demonstrates that plastid loss is more common than previously thought. Issue Section: Discoveries

evolutionary biology↗

bioRxiv2024

Time-dependent effects of species interactions at macroevolutionary scale shape the diversity of mimetic butterflies.

Evidence that species interactions can affect macroevolutionary dynamics of trait and species diversification is scarce. Mutualistic Mullerian mimicry is a compelling example of example of ecological interactions that has been shown to drive evolutionary convergence, Here, we test how mutualistic Mullerian mimicry shapes macroevolutionary patterns of diversification in the Ithomiini butterflies. We show that the age of color patterns is the primary determinant of species richness within mimicry rings but not phylogenetic diversity. We find pervasive phylogenetic signal in mimicry rings and in color patterns associated within polymorphic species. Only a small set of mimicry rings show high phylogenetic diversity. We identify patterns of saturation in the accumulation of new mimicry rings and in the number of evolutionary convergences towards the most species-rich mimicry rings. Those saturation patterns are likely caused by niche filling along various ecological dimensions, within and among the mimetic communities living in sympatry. The time-dependent effects detected in our study illustrate how neutral processes and ecological interactions interact and shape species and phenotypic diversification.

evolutionary biology↗

bioRxiv2024

Freshwater "microcroissants" shed light on a novel higher-level clade within Trebouxiophyceae and reveal the genus Chlorolobion as a trebouxiophyte

Trebouxiophyceae is a widespread and species-rich green algal class encompassing mostly coccoid algae with a simple ovoid or ellipsoidal outline. However, some poorly-sampled lineages have evolved more elaborate shapes or even complex thalli, adding to the classs morphological diversity. Led by new and previously established strains, this study additionally uncovered a clade of croissant-like trebouxiophytes. Phylogenetic analyses inferred from nuclear 18S rDNA and chloroplast rbcL sequences confirmed the monophyly of the microcroissant clade, which we propose to be classified as a new family, Ragelichloridaceae. This family includes two novel genera, Ragelichloris and Navichloris, and the previously described Thorsmoerkia. The position of Ragelichloridaceae within Trebouxiophyceae stayed unresolved but chloroplast phylogenomics showed that the family belongs to the broader incertae sedis group, which also includes Xylochloris and Leptosira. In addition, our study showed that the microcroissant-like genus Chlorolobion, previously classified within Chlorophyceae, is a genuine trebouxiophyte, potentially related to Ragelichloridaceae. HighlightsO_LIA new family-level clade uncovered within Trebouxiophyceae. C_LIO_LITwo new genera described. C_LIO_LIThe genus Chlorolobion shown to be a trebouxiophyte. C_LI

plant biology↗