Among vertebrates, nearly all oviparous animals are considered to have either obligate aquatic or terrestrial oviposition, with eggs that are specialized for developing in those environments. The terrestrial environment has considerably more oxygen but is dry and thus presents both opportunities and challenges for developing embryos, particularly those adapted for aquatic development. Here, we present evidence from field experiments examining egg-laying behavior, egg size, and egg jelly function of 13 species of Central and South American treefrogs in the genus Dendropsophus, which demonstrates that flexible oviposition (individuals laying eggs both in and out of water) and eggs capable of both aquatic and terrestrial development are the likely factors which enable the transition from aquatic to terrestrial reproduction. Nearly half of the species we studied had previously undescribed degrees of flexible oviposition. Species with obligate terrestrial reproduction have larger eggs than species with aquatic reproduction, and species with flexible reproduction have eggs of intermediate sizes. Obligate terrestrial breeding frogs also have egg masses that absorb water more quickly than those with flexible oviposition. We also examined eight populations of a single species, Dendropsophus ebraccatus, and document substantial intraspecific variation in terrestrial oviposition; populations in rainy, stable climates lay fewer eggs in water than those in drier areas. However, no differences in egg size were found, supporting the idea that the behavioral component of oviposition evolves before other adaptations associated with obligate terrestrial reproduction. Collectively, these data demonstrate the key role that behavior can have in facilitating major evolutionary transitions.

BACKGROUND: Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea.
RESULTS: Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group.
CONCLUSIONS: We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

The conquest of land by plants was concomitant with, and possibly enabled by, the evolution of three-dimensional (3D) growth. The moss Physcomitrium patens provides a model system for elucidating molecular mechanisms in the initiation of 3D growth. Here, we investigate whether the phytohormone ethylene, which is believed to have been a signal before land plant emergence, plays a role in 3D growth regulation in P. patens. We report ethylene controls 3D gametophore formation, based on results from exogenously applied ethylene and genetic manipulation of PpEIN2, which is a central component in the ethylene signaling pathway. Overexpression (OE) of PpEIN2 activates ethylene responses and leads to earlier formation of gametophores with fewer gametophores produced thereafter, phenocopying ethylene-treated wild-type. Conversely, Ppein2 knockout mutants, which are ethylene insensitive, show initially delayed gametophore formation with more gametophores produced later. Furthermore, pharmacological and biochemical analyses reveal auxin levels are decreased in the OE lines but increased in the knockout mutants. Our results suggest that evolutionarily, ethylene and auxin molecular networks were recruited to build the plant body plan in ancestral land plants. This might have played a role in enabling ancient plants to acclimate to the continental surfaces of the planet.

We propose that the global environmental crises of the Anthropocene are the outcome of a ratcheting process in long-term human evolution which has favoured groups of increased size and greater environmental exploitation. To explore this hypothesis, we review the changes in the human ecological niche. Evidence indicates the growth of the human niche has been facilitated by group-level cultural traits for environmental control. Following this logic, sustaining the biosphere under intense human use will probably require global cultural traits, including legal and technical systems. We investigate the conditions for the evolution of global cultural traits. We estimate that our species does not exhibit adequate population structure to evolve these traits. Our analysis suggests that characteristic patterns of human group-level cultural evolution created the Anthropocene and will work against global collective solutions to the environmental challenges it poses. We illustrate the implications of this theory with alternative evolutionary paths for humanity. We conclude that our species must alter longstanding patterns of cultural evolution to avoid environmental disaster and escalating between-group competition. We propose an applied research and policy programme with the goal of avoiding these outcomes. This article is part of the theme issue \'Evolution and sustainability: gathering the strands for an Anthropocene synthesis\'.

Smell abilities differ greatly among vertebrate species due to distinct sensory needs, with exceptional variability reported in the number of olfactory genes and the size of the odour-processing regions of the brain. However, key environmental factors shaping genomic and phenotypic changes linked to the olfactory system remain difficult to identify at macroevolutionary scales. Here, we investigate the association between diverse ecological traits and the number of olfactory chemoreceptors in approximately two hundred ray-finned fishes.
We found independent expansions producing large gene repertoires in several lineages of nocturnal amphibious fishes, generally able to perform active terrestrial exploration. We reinforced this finding with on-purpose genomic and transcriptomic analysis of Channallabes apus, a catfish species from a clade with chemosensory-based aerial orientation. Furthermore, we also detected an augmented information-processing capacity in the olfactory bulb of nocturnal amphibious fishes by estimating the number of cells contained in this brain region in twenty-four actinopterygian species.
Overall, we report a convergent genomic and phenotypic magnification of the olfactory system in nocturnal amphibious fishes. This finding suggests the possibility of an analogous evolutionary event in fish-like tetrapod ancestors during the first steps of the water-to-land transition, favouring terrestrial adaptation through enhanced aerial orientation.

Pollinator shifts are often related to speciation in angiosperms, and the relationship between them has been discussed in several plant taxa. Although limited information on plants pollinated by non-flying mammals in Central and South America and Africa is available, related research has not been conducted in Asia. Herein, I summarize the available knowledge of pollination in Asian Mucuna (Fabaceae), a genus mainly distributed in the tropics, and discuss the evolution of plants pollinated by non-flying mammals in Asia. Nineteen pollinator species have been recorded and pollination systems have been categorized into four types. An examination of the relationship between Mucuna species and their pollinators from the lineage perspective revealed that all species in Mucuna, subgenus Macrocarpa, which are distributed in Asia, are pollinated exclusively by non-flying mammals. Additionally, plants pollinated by non-flying mammals were found to have diverged from bat-pollinated and non-flying mammal-pollinated plants, while plants pollinated by non-flying mammals have evolved multiple times. This is a unique example of evolutionary transition. I hypothesize that the diversification of squirrel species in tropical Asia may have led to the speciation and diversification of Mucuna in Asia. Furthermore, the behavioural and ecological characteristics of bats and birds in Asia differ from the characteristics of those in other regions, implying that Asian Mucuna species do not rely on bat or bird pollinators. The adaptation of floral characteristics to pollinators is not well understood in Asia. Mammal-pollinated plants in Asia may have evolved differently from those in other regions and have unique pollination systems.

Adaptations of ciliates to hypoxic environments have arisen independently several times. Studies on mitochondrion-related organelle (MRO) metabolisms from distinct anaerobic ciliate groups provide evidence for understanding the transitions from mitochondria to MROs within eukaryotes. To deepen our knowledge about the evolutionary patterns of ciliate anaerobiosis, mass-culture and single-cell transcriptomes of two anaerobic species, Metopus laminarius (class Armophorea) and Plagiopyla cf. narasimhamurtii (class Plagiopylea), were sequenced and their MRO metabolic maps were compared. In addition, we carried out comparisons using publicly available predicted MRO proteomes from other ciliate classes (i.e., Armophorea, Litostomatea, Muranotrichea, Oligohymenophorea, Parablepharismea and Plagiopylea). We found that single-cell transcriptomes were similarly comparable to their mass-culture counterparts in predicting MRO metabolic pathways of ciliates. The patterns of the components of the MRO metabolic pathways might be divergent among anaerobic ciliates, even among closely related species. Notably, our findings indicate the existence of group-specific functional relics of electron transport chains (ETCs). Detailed group-specific ETC functional patterns are as follows: full oxidative phosphorylation in Oligohymenophorea and Muranotrichea; only electron-transfer machinery in Armophorea; either of these functional types in Parablepharismea; and ETC functional absence in Litostomatea and Plagiopylea. These findings suggest that adaptation of ciliates to anaerobic conditions is group-specific and has occurred multiple times. Our results also show the potential and the limitations of detecting ciliate MRO proteins using single-cell transcriptomes and improve the understanding of the multiple transitions from mitochondria to MROs within ciliates.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s42995-022-00147-w.

Processes of evolutionary transition (ET), becoming part of a new reproducing collective while losing the capacity of independent reproduction, seem difficult to track without circularity, since their features-units of selection, individuality, inheritance at multiple levels (MLS1, MLS2)-are products of one process. We describe ET in a non-circular way, noting kinds of interactions among community members necessary for such major transitions that are not instances of those same interactions within community members. Reproducing \'systems\' tend to hybridize with environmental components, employing eco-devo scaffolding interactions forming communities. Communities are developmentally scaffolded systems of diverse members engaged in heterogeneous interactions. They may become individuals in their own right with the potential to evolve an inheritance system at the emergent community level. We argue for the explanatory benefits of treating \'individuality\' as a special case of \'collectivity\'. We characterize an idealized sequence of collective processes-coordination, cooperation and collaboration (3Cs)-which scaffolds transitions to new forms of collective individuality: communities. Hominid evolution and learning draw attention to developmental interactions driving both dimensions of ET: new \'levels of individuality\' and inherited \'information systems\'. Here, we outline a theoretical perspective that we suggest applies across a wide range of cases and scenarios. This article is part of the theme issue \'Human socio-cultural evolution in light of evolutionary transitions\'.

The emergence of animal societies is a major evolutionary transition, but its implications for learning-dependent innovations are insufficiently understood. Bees, with lifestyles ranging from solitary to eusocial, are ideal models for exploring social evolution. Here, we ask how and why bees may acquire a new \'technology\', foraging on morphologically complex flowers, and whether eusociality facilitates this technological shift. We consider \'complex\' flowers that produce high food rewards but are difficult to access, versus \'simple\' flowers offering easily accessible yet lower rewards. Complex flowers are less profitable than simple flowers to naive bees but become more rewarding after a learning period. We model how social bees optimally choose between simple and complex flowers over time, to maximize their colony\'s food balance. The model predicts no effect of colony size on the bees\' flower choices. More foraging on complex flowers is predicted as colony longevity, its proportion of foragers, individual longevity and learning ability increase. Of these traits, only long-lived colonies and abundant foragers characterize eusocial bees. Thus, we predict that eusociality supports, but is not mandatory for, learning to exploit complex flowers. A re-analysis of a large published dataset of bee-flower interactions supports these conclusions. We discuss parallels between the evolution of insect sociality and other major transitions that provide scaffolds for learning innovations. This article is part of the theme issue \'Human socio-cultural evolution in light of evolutionary transitions\'.

The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures of the transition to the ECM habit within the hyper-diverse Russulaceae. We present comparative analyses of the genomic architecture and the total and secreted gene repertoires of 18 species across the order Russulales of which 13 are newly sequenced, including a representative of a saprotrophic member of Russulaceae, Gloeopeniophorella convolvens. The genomes of ECM Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of small secreted proteins (SSPs) with TE \"nests\", or dense aggregations of TEs. Some PCWDEs have been retained or even expanded, mostly in a species-specific manner. The genome of Gloeopeniophorella convolvens possesses some characteristics of ECM genomes (e.g., loss of some PCWDEs, TE expansion, reduction in secondary metabolism clusters). Functional specialization in ectomycorrhizal decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ECM habit, indicating that changes in genome architecture and gene content may be necessary to prime the evolutionary switch.