Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs

Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs frequently contain binding motifs for transcription factors and capture binding motifs during transposition, which they spread through the genome by transposition. Thus, TEs drive the evolution and diversification of gene regulatory networks by recruiting lineage-specific targets under the regulatory control of specific transcription factors. This process can explain the rapid and repeated evolution of developmental novelties, such as C4 photosynthesis and a wide spectrum of stress responses in plants. It also underpins the convergent evolution of embryo nourishing tissues, the placenta in mammals and the endosperm in flowering plants. Furthermore, the gene regulatory network underlying flower development has also been largely reshaped by TE-mediated recruitment of regulatory elements; some of them being preserved across long evolutionary timescales. In this review, we highlight the potential role of TEs as evolutionary toolkits in plants by showcasing examples of TE-mediated evolutionary novelties.

Venom Systems as Models for Studying the Origin and Regulation of Evolutionary Novelties

A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to perform the same function, that is, produce and deliver a cocktail of potent molecules to subdue prey or predators. Venomous organisms therefore offer unique opportunities to investigate the evolutionary processes of convergence of key adaptive traits, and the molecular mechanisms underlying the emergence of novel genes, cells, and tissues. Indeed, some venomous species have already proven to be highly amenable as models for developmental studies, and recent work with venom gland organoids provides manipulatable systems for directly testing important evolutionary questions. Here, we provide a synthesis of the current knowledge that could serve as a starting point for the establishment of venom systems as new models for evolutionary and molecular biology. In particular, we highlight the potential of various venomous species for the study of cell differentiation and cell identity, and the regulatory dynamics of rapidly evolving, highly expressed, tissue-specific, gene paralogs. We hope that this review will encourage researchers to look beyond traditional study organisms and consider venom systems as useful tools to explore evolutionary novelties.

The Evolutionary Road to Human Memory

We tend to think about memory in terms of our own experience, but a series of our direct ancestors—from the earliest vertebrates to archaic humans—also had memories. The evolutionary history that we share with these ancestral species has left its mark on modern memory, complemented by other forms of memory that are uniquely human. This book traces the long evolutionary road to human memory by explaining how a series of now-extinct ancestral species adapted to life in their world, in their time and place. As they did, new brain areas appeared, each of which supported an innovative form of memory that helped them gain an advantage in life. Through inheritance and modification across millions of years, these evolutionary novelties created several kinds of memory that influence the human mind today. Then, during human evolution, yet another new kind of memory emerged: about ourselves and others. This evolutionary innovation ignited human imagination; empowered us to remember and talk about a personal past; and enabled the sharing of knowledge about our world, our cultures, and ourselves. Through these developments, evolution made it possible for every individual, day upon day, to add new pages to the story of a life: the remarkable, rich record of experiences and knowledge that make up a human mind.

Phylogeny of Macronematinae (Trichoptera: Hydropsychidae) based on molecular and morphological analyses

The phylogenetic relationships among the members of Macronematinae (Trichoptera: Hydropsychidae) have long been debated and often revised. Our study based on a large subunit (28S) nuclear ribosomal DNA (D2 expansion fragment; 464 base pairs) of gene sequences found all genera to be monophyletic except for the genus Polymorphanisus Walker, which produced two clades in accordance with its species groups established using morphological characters. Phylogenetic reconstruction based on mitochondrial cytochrome oxidase I (658 base pairs) found the same monophyletic relationships, however, except for the genera Polymorphanisus and Macrostemum Kolenati. The placement of the genus Leptonema Guérin-Méneville as the basal clade in the subfamily was also ruled out, which is consistent with previous morphological findings. The monophyly of two previously recognised tribes (Macronematini and Polymorphanisini) was not supported. We also found that the genera Centromacronema Ulmer, Baliomorpha Neboiss, and Macronema Pictet are most closely related, having three head setal warts on the vertex of the head and unsegmented inferior appendages of male genitalia as their synapomorphies. Our study supported the hypothesis of close relationship of the genera Amphipsyche McLachlan and Protomacronema Ulmer with the morphological synapomorphies: absence of a forewing discoidal cell and the presence of elevated head carinae on the larvae. Some notable evolutionary novelties in the structure of adults in various lineages of this subfamily include reduction of maxillae and labium, reduction and loss of a discoidal cell and evolution of a c-sc crossvein in each forewing, fusion of segments in each male inferior appendage, and evolution of dark colour patterns in the forewings. Also, the head setal warts, which are unique organs in Trichoptera, evolved towards a decreasing number in the subfamily. This first molecular phylogenetic study, covering most genera in Macronematinae and including an interpretation of 12 key evolutionary novelties, provides an important basis for resolving long-standing questions regarding phylogenetic relationships and classification of genera and species and helps lay a stronger foundation for inference of testable hypotheses about functional traits for species of this common and widespread subfamily.

Evidence for a giant parrot from the Early Miocene of New Zealand

Insular avifaunas have repeatedly spawned evolutionary novelties in the form of unusually large, often flightless species. We report fossils from the Early Miocene St Bathans Fauna of New Zealand that attests to the former existence of a giant psittaciform, which is described as a new genus and species. The fossils are two incomplete tibiotarsi from a bird with an estimated mass of 7 kg, double that of the heaviest known parrot, the kakapo Strigops habroptila . These psittaciform fossils show that parrots join the growing group of avian taxa prone to giantism in insular species, currently restricted to palaeognaths, anatids, sylviornithids, columbids, aptornithids, ciconiids, tytonids, falconids and accipitrids.

How to Investigate the Origins of Novelty: Insights Gained from Genetic, Behavioral, and Fitness Perspectives

Synopsis Biologists are drawn to the most extraordinary adaptations in the natural world, often referred to as evolutionary novelties, yet rarely do we understand the microevolutionary context underlying the origins of novel traits, behaviors, or ecological niches. Here we discuss insights gained into the origins of novelty from a research program spanning biological levels of organization from genotype to fitness in Caribbean pupfishes. We focus on a case study of the origins of novel trophic specialists on San Salvador Island, Bahamas and place this radiation in the context of other rapid radiations. We highlight questions that can be addressed about the origins of novelty at different biological levels, such as measuring the isolation of novel phenotypes on the fitness landscape, locating the spatial and temporal origins of adaptive variation contributing to novelty, detecting dysfunctional gene regulation due to adaptive divergence, and connecting behaviors with novel traits. Evolutionary novelties are rare, almost by definition, and we conclude that integrative case studies can provide insights into this rarity relative to the dynamics of adaptation to more common ecological niches and repeated parallel speciation, such as the relative isolation of novel phenotypes on fitness landscapes and the transient availability of ecological, genetic, and behavioral opportunities.

Identity and novelty in the avian syrinx

In its most basic conception, a novelty is simply something new. However, when many previously proposed evolutionary novelties have been illuminated by genetic, developmental, and fossil data, they have refined and narrowed our concept of biological “newness.” For example, they show that these novelties can occur at one or multiple levels of biological organization. Here, we review the identity of structures in the avian vocal organ, the syrinx, and bring together developmental data on airway patterning, structural data from across tetrapods, and mathematical modeling to assess what is novel. In contrast with laryngeal cartilages that support vocal folds in other vertebrates, we find no evidence that individual cartilage rings anchoring vocal folds in the syrinx have homology with any specific elements in outgroups. Further, unlike all other vertebrate vocal organs, the syrinx is not derived from a known valve precursor, and its origin involves a transition from an evolutionary “spandrel” in the respiratory tract, the site where the trachea meets the bronchi, to a target for novel selective regimes. We find that the syrinx falls into an unusual category of novel structures: those having significant functional overlap with the structures they replace. The syrinx, along with other evolutionary novelties in sensory and signaling modalities, may more commonly involve structural changes that contribute to or modify an existing function rather than those that enable new functions.