Improving phylogenetic resolution of the Lamiales using the complete plastome sequences of six Penstemon species

The North American endemic genus Penstemon (Mitchell) has a recent geologic origin of ca. 3.6 million years ago (MYA) during the Pliocene/Pleistocene transition and has undergone a rapid adaptive evolutionary radiation with ca. 285 species of perennial forbs and sub-shrubs. Penstemon is divided into six subgenera occupying all North American habitats including the Arctic tundra, Central American tropical forests, alpine meadows, arid deserts, and temperate grasslands. Due to the rapid rate of diversification and speciation, previous phylogenetic studies using individual and concatenated chloroplast sequences have failed to resolve many polytomic clades. We investigated the efficacy of utilizing the plastid genomes (plastomes) of 29 species in the Lamiales order, including five newly sequenced Penstemon plastomes, for analyzing phylogenetic relationships and resolving problematic clades. We compared whole-plastome based phylogenies to phylogenies based on individual gene sequences (matK, ndhF, psaA, psbA, rbcL, rpoC2, and rps2) and concatenated sequences. We also We found that our whole-plastome based phylogeny had higher nodal support than all other phylogenies, which suggests that it provides greater accuracy in describing the hierarchal relationships among taxa as compared to other methods. We found that the genus Penstemon forms a monophyletic clade sister to, but separate from, the Old World taxa of the Plantaginaceae family included in our study. Our whole-plastome based phylogeny also supports the rearrangement of the Scrophulariaceae family and improves resolution of major clades and genera of the Lamiales.

New Biochronological Scales of Planktic Foraminifera for the Early Danian Based on High-Resolution Biostratigraphy

After the Cretaceous/Paleogene boundary (KPB) catastrophic mass extinction event, an explosive evolutionary radiation of planktic foraminifera took place in consequence of the prompt occupation of empty niches. The rapid evolution of new species makes it possible to establish high-resolution biozonations in the lower Danian. We propose two biostratigraphic scales for low-to-middle latitudes spanning the first two million years of the Danian. The first is based on qualitative data and includes four biozones: the Guembelitria cretacea Zone (Dan1), the Parvularugoglobigerina longiapertura Zone (Dan2), the Parvularugoglobigerina eugubina Zone (Dan3), and the Parasubbotina pseudobulloides Zone (Dan4). The latter two are divided into several sub-biozones: the Parvularugoglobigerina sabina Subzone (Dan3a) and the Eoglobigerina simplicissima Subzone (Dan3b) for the Pv. eugubina Zone, and the Praemurica taurica Subzone (Dan4a), the Subbotina triloculinoides Subzone (Dan4b), and the Globanomalina compressa Subzone (Dan4c) for the P. pseudobulloides Zone. The second scale is based on quantitative data and includes three acme-zones (abundance zones): the Guembelitria Acme-zone (DanAZ1), the Parvularugoglobigerina-Palaeoglobigerina Acme-zone (DanAZ2), and the Woodringina-Chiloguembelina Acme-zone (DanAZ3). Both biozonations are based on high-resolution samplings of the most continuous sections of the lower Danian worldwide and have been calibrated with recent magnetochronological and astrochronological dating.

CyanoHABs: unavoidable evolutionary ecological consequence for low nutrient-requiring cyanobacteria in eutrophic water

The mechanism of cyanobacterial harmful algal blooms (CyanoHABs) is complicated and confusing. One major reason is they are studied primarily from an ecological perspective and on bloom-forming species only. This narrow angle loses a broader evolutionary and ecological context in which CyanoHABs occur and fails to provide information on relevant components to achieve a wholistic understanding. To derive a comprehensive mechanism of CyanoHABs, we examine CyanoHABs through the overlooked evolutionary and ecological lenses: evolutionary radiation, ecological comparison with co-living algae, and recently identified genomic functional repertoire between blooming and non-blooming species. We found key factors: (1) elaborate diverse functional repertoire and low nutrient requirement in cyanobacteria molded by early adaptive evolution, (2) cyanobacteria having lower nutrient requirements than green algae indeed, (3) there is no directed evolution in biological functions toward water eutrophication in cyanobacteria, (4) the CyanoHAB-associated functional repertoire are more abundant and complete in blooming than non-blooming species. These factors lead us to postulate a preliminary mechanism of CyanoHABs as a synergistic quad: superior functional repertoire, established with long adaptive radiation under nutrient-deficient conditions and not evolved toward eutrophic conditions, enables cyanobacteria to efficiently utilize elevated nutrients under current eutrophic regime for excess growth and CyanoHABs thereof, due to their lower nutrient requirements than co-living algae. This preliminary synthesis without doubt needs further empirical testing, which can be undertaken with more comparative studies of multiple species using integrated systems biology approaches.

Photosynthetic activity in Devonian Foraminifera

Photosynthetically active foraminifera are prolific carbonate producers in warm, sunlit, surface waters of the oceans. Foraminifera have repeatedly developed mixotrophic strategies (i.e., the ability of an organism or holobiont to both feed and photosynthesize) by facultative or obligate endosymbiosis with microalgae or by sequestering plastids (kleptoplasts) of ingested algae. Mixotrophy provides access to essential nutrients (e.g., N, P) through feeding while providing carbohydrates and lipids produced through photosynthesis, resulting in substantial energetic advantage in warm, sunlit environments where food and dissolved nutrients are scarce. Our morphological as well as stable carbon isotope data provide, as of now, the earliest (Mid-Devonian) evidence for photosynthetic activity in the first advanced, multichambered, calcareous foraminifera, Semitextularia, from the tropical shelf of the Laurussia paleocontinent. This adaptation likely influenced the evolutionary radiation of calcareous Foraminifera in the Devonian (“Givetian revolution”), one of the most important evolutionary events in foraminiferal history, that coincided with the worldwide development of diverse calcifying marine communities inhabiting shelf environments linked with Devonian stromatoporoid coral reefs.

Muscle systems and motility of early animals highlighted by cnidarians from the basal Cambrian

Although fossil evidence suggest that various animal groups were able to move actively through their environment in the early stages of their evolution, virtually no direct information is available on the nature of their muscle systems. The origin of jellyfish swimming, for example, is of great concern to biologists. Exceptionally preserved muscles are described here in benthic peridermal olivooid medusozoans from the basal Cambrian of China (Kuanchuanpu Formation, ca. 535 Ma) that have direct equivalent in modern medusozoans. They consist of circular fibers distributed over the bell surface (subumbrella) and most probably have a myoepithelial origin. This is the oldest record of a muscle system in cnidarians and more generally in animals. This basic system was probably co-opted by younger early Cambrian jellyfish to develop capacities for the jet-propelled swimming within the water column. Additional lines of fossil evidence obtained from ecdysozoans (worms and panarthropods) show that the muscle systems of early animals underwent a rapid diversification through the early Cambrian and increased their capacity to colonize a wide range of habitats both within the water column and sediment at a critical time of their evolutionary radiation.

Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade

Islands have long been recognized as key contributors to biodiversity because they facilitate geographic isolation and ecological divergence from mainland ancestors. However, island colonization has traditionally been considered an evolutionary dead-end process, and its consequences for continental biodiversity remain understudied. Here, we use the evolutionary radiation of Columbiformes (i.e. pigeons and doves) to examine if ecological niche shifts on islands shaped biological diversification and community composition on continents. We show that the colonization of islands by continental, terrestrial-foraging lineages led to the exploitation of a new ecological niche (i.e. arboreal foraging). This transition towards arboreal foraging was associated with evolutionary adaptation towards a new morphological optimum. In addition, arboreal-foraging lineages of islands experienced an increase in speciation rates, which was associated with successful range expansions to other islands as well as back colonization of continents. Our results provide empirical evidence that diversification on continents can only be fully understood when studying the diversification processes that took place on islands, challenging the view of islands as mere sinks of evolutionary diversity.

A reassessment of the enigmatic diapsid Paliguana whitei and the early history of Lepidosauromorpha

Lepidosaurs include lizards, snakes, amphisbaenians and the tuatara, comprising a highly speciose evolutionary radiation with widely varying anatomical traits. Their stem-lineage originated by the late middle Permian 259 million years ago, but its early fossil record is poorly documented, obscuring the origins of key anatomical and functional traits of the group. Paliguana whitei , from the Early Triassic of South Africa, is an enigmatic fossil species with the potential to provide information on this. However, its anatomy and phylogenetic affinities remain highly uncertain, and have been debated since its discovery more than 100 years ago. We present microtomographic three-dimensional imaging of the cranial anatomy of P. whitei that clarifies these uncertainties, providing strong evidence for lepidosauromorph affinities based on the structure of the temporal region and the implantation of marginal dentition. Phylogenetic analysis including these new data recovers Paliguana as the earliest known stem-lepidosaur, within a long-lived group of early diverging lepidosauromorphs that persisted to at least the Middle Jurassic. Our results provide insights into cranial evolution on the lepidosaur stem-lineage, confirming that characteristics of pleurodont dental implantation evolved early on the lepidosaur stem-lineage. By contrast, key functional traits related to hearing (quadrate conch) and feeding (streptostyly) evolved later in the lepidosaur crown-group.

Linking the genomic signatures of human beat synchronization and learned song in birds

The development of rhythmicity is foundational to communicative and social behaviours in humans and many other species, and mechanisms of synchrony could be conserved across species. The goal of the current paper is to explore evolutionary hypotheses linking vocal learning and beat synchronization through genomic approaches, testing the prediction that genetic underpinnings of birdsong also contribute to the aetiology of human interactions with musical beat structure. We combined state-of-the-art-genomic datasets that account for underlying polygenicity of these traits: birdsong genome-wide transcriptomics linked to singing in zebra finches, and a human genome-wide association study of beat synchronization. Results of competitive gene set analysis revealed that the genetic architecture of human beat synchronization is significantly enriched for birdsong genes expressed in songbird Area X (a key nucleus for vocal learning, and homologous to human basal ganglia). These findings complement ethological and neural evidence of the relationship between vocal learning and beat synchronization, supporting a framework of some degree of common genomic substrates underlying rhythm-related behaviours in two clades, humans and songbirds (the largest evolutionary radiation of vocal learners). Future cross-species approaches investigating the genetic underpinnings of beat synchronization in a broad evolutionary context are discussed. This article is part of the theme issue ‘Synchrony and rhythm interaction: from the brain to behavioural ecology’.