The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Evolution and expansion of the RUNX2 QA repeat corresponds with the emergence of vertebrate complexity

Runt-related transcription factor 2 (RUNX2) is critical for the development of the vertebrate bony skeleton. Unlike other RUNX family members, RUNX2 possesses a variable poly-glutamine, poly-alanine (QA) repeat domain. Natural variation within this repeat is able to alter the transactivation potential of RUNX2, acting as an evolutionary ‘tuning knob’ suggested to influence mammalian skull shape. However, the broader role of the RUNX2 QA repeat throughout vertebrate evolution is unknown. In this perspective, we examine the role of the RUNX2 QA repeat during skeletal development and discuss how its emergence and expansion may have facilitated the evolution of morphological novelty in vertebrates.

Heterochronic origin of spherical fusulinid foraminifera in the late Paleozoic

Heterochrony describes acceleration, displacement, and/or retardation of descendants’ development events compared with ancestral states and has often been cited as an important process to bring about morphological novelty. It was coined one-and-a-half centuries ago and has been discussed by both paleobiologists and biologists frequently ever since. Many types of fossil organisms preserve aspects of their development histories in their bones or shells that have been used for heterochrony analyses, with body size being used as a developmental age indicator, despite questions being raised regarding this practice. For organisms whose hard structures consist of multiple chambers, or that contain growth lines, age information suggested by these structures independently can facilitate ontogenetic modeling. In this way, relations among size, shape, and age can be established to document patterns of morphological development. Morphological analysis of pseudoschwagerine fusulinids, a fossil foraminifera group that developed a morphologically novel spherical shell, along with their presumptive triticitid ancestors illustrates this approach to heterochrony analysis. Ontogenetic trajectory comparisons of four major pseudoschwagerine genera, as well as those of triticitids, document relations between their shapes, sizes, and developmental ages. A complex of heterochronic patterns, including peramorphic predisplacement, hypermorphosis, and acceleration, characterize pseudoschwagerine development and appear to be responsible for the novel appearance of large, inflated fusiform and spherical tests in these late Paleozoic benthic foraminifera. The morphometric approach employed in this investigation could be applied widely in the quantitative morphological studies of development histories in a variety of other fossil groups.

Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure

One of the fundamental gaps in our knowledge of how novel anatomical structures evolve is understanding the origins of the morphogenetic processes that form these features. Here, we traced the cellular development of a recently evolved morphological novelty, the posterior lobe of D. melanogaster. We found that this genital outgrowth forms through extreme increases in epithelial cell height. By examining the apical extracellular matrix (aECM), we also uncovered a vast matrix associated with the developing genitalia of lobed and non-lobed species. Expression of the aECM protein Dumpy is spatially expanded in lobe-forming species, connecting the posterior lobe to the ancestrally derived aECM network. Further analysis demonstrated that Dumpy attachments are necessary for cell height increases during posterior lobe development. We propose that the aECM presents a rich reservoir for generating morphological novelty and highlights a yet unseen role for aECM in regulating extreme cell height.

Multiple Plasticity Regulators Reveal Targets Specifying an Induced Predatory Form in Nematodes

The ability to translate a single genome into multiple phenotypes, or developmental plasticity, defines how phenotype derives from more than just genes. However, to study the evolutionary targets of plasticity and their evolutionary fates, we need to understand how genetic regulators of plasticity control downstream gene expression. Here, we have identified a transcriptional response specific to polyphenism (i.e., discrete plasticity) in the nematode Pristionchus pacificus. This species produces alternative resource-use morphs—microbivorous and predatory forms, differing in the form of their teeth, a morphological novelty—as influenced by resource availability. Transcriptional profiles common to multiple polyphenism-controlling genes in P. pacificus reveal a suite of environmentally sensitive loci, or ultimate target genes, that make up an induced developmental response. Additionally, in vitro assays show that one polyphenism regulator, the nuclear receptor NHR-40, physically binds to promoters with putative HNF4α (the nuclear receptor class including NHR-40) binding sites, suggesting this receptor may directly regulate genes that describe alternative morphs. Among differentially expressed genes were morph-limited genes, highlighting factors with putative “on–off” function in plasticity regulation. Further, predatory morph-biased genes included candidates—namely, all four P. pacificus homologs of Hsp70, which have HNF4α motifs—whose natural variation in expression matches phenotypic differences among P. pacificus wild isolates. In summary, our study links polyphenism regulatory loci to the transcription producing alternative forms of a morphological novelty. Consequently, our findings establish a platform for determining how specific regulators of morph-biased genes may influence selection on plastic phenotypes.

Expansion of apical extracellular matrix underlies the morphogenesis of a recently evolved structure

One of the fundamental gaps in our knowledge of the evolution of novel structures is understanding how the morphogenetic processes that form these structures arise. Here, we traced the cellular development of a morphological novelty, the posterior lobe of D. melanogaster. We found that this genital outgrowth forms through an extreme increase in cell height. By examining the apical extracellular matrix (aECM), we uncovered a vast network associated with the developing genitalia of lobed and non-lobed species. We observed that cells which will form the posterior lobe show expanded expression of the aECM protein Dumpy which connects them to the ancestral aECM network. Further analysis demonstrated a required role for Dumpy in cell height increase during development. We propose that the aECM presents a rich reservoir for generating morphological novelty, in addition to highlighting a yet unseen role for aECM in regulating extreme cell height.

Evolutionary parallelisms of pectoral and pelvic network-anatomy from fins to limbs

Lobe-fins transformed into limbs during the Devonian period, facilitating the water-to-land transition in tetrapods. We traced the evolution of well-articulated skeletons across the fins-to-limbs transition, using a network-based approach to quantify and compare topological features of fins and limbs. We show that the topological arrangement of bones in pectoral and pelvic appendages evolved in parallel during the fins-to-limbs transition, occupying overlapping regions of the morphospace, following a directional trend, and decreasing their disparity over time. We identify the presence of digits as the morphological novelty triggering topological changes that discriminated limbs from fins. The origin of digits caused an evolutionary shift toward appendages that were less densely and heterogeneously connected, but more assortative and modular. Disparity likewise decreased for both appendages, more markedly until a time concomitant with the earliest-known tetrapod tracks. Last, we rejected the presence of a pectoral-pelvic similarity bottleneck at the origin of tetrapods.

Evolution of leaf-cutter behavior in bees (Hymenoptera: Megachilidae) as inferred from total-evidence tip-dating analyses

A unique feature among bees is the ability of some species ofMegachile s.l. to cut and process fresh leaves for nest construction. The presence of razors between the female mandibular teeth (interdental laminae) to facilitate leaf-cutting (LC) is a morphological novelty that might have triggered a subsequent diversification in this group. However, we have a limited understanding of the evolutionary origins of this behavior and associated structures. Herein, we use total-evidence tip-dating analyses to infer the origin of LC bees and patterns of variation of interdental laminae. Our datasets included five nuclear genes, representatives of all fossil taxa, 80% of the extant generic-level diversity of Megachilidae, and the full range of generic and subgeneric diversity of Megachilini. Our analyses support the notion of a recent origin of LC bees (15–25 Ma), casting doubts on Eocene trace fossils attributed to these bees. We demonstrate that interdental laminae developed asynchronicaly from two different structures in the mandible (teeth or fimbrial ridge), and differ in their phenotypic plasticity. Based on the phylogenetic results, we propose robust classificatory solutions to long-standing challenges in the systematics of Megachilidae. We discuss the implications of our findings as a foundational framework to develop novel evolutionary, ecological, and functional hypotheses on this behavior.