Landscape of human spinal cord cell type diversity at midgestation

Understanding spinal cord generation and assembly is essential to elucidate how motor behavior is controlled and how disorders arise. The cellular landscape of the human spinal cord remains, however, insufficiently explored. Here, we profiled the midgestation human spinal cord with single cell-resolution and discovered, even at this fetal stage, remarkable heterogeneity across and within cell types. Glia displayed diversity related to positional identity along the dorso-ventral and rostro-caudal axes, while astrocytes with specialized transcriptional programs mapped onto distinct histological domains. We discovered a surprisingly early diversification of alpha (α) and gamma (γ) motor neurons that control and modulate contraction of muscle fibers, which was suggestive of accelerated developmental timing in human spinal cord compared to rodents. Together with mapping of disease-related genes, this transcriptional profile of the developing human spinal cord opens new avenues for interrogating the cellular basis of motor control and related disorders in humans.

Interstitial Arabidopsis-Type Telomeric Repeats in Asteraceae

Tandem repeats of telomeric-like motifs at intra-chromosomal regions, known as interstitial telomeric repeats (ITR), have drawn attention as potential markers of structural changes, which might convey information about evolutionary relationships if preserved through time. Building on our previous work that reported outstanding ITR polymorphisms in the genus Anacyclus, we undertook a survey across 132 Asteraceae species, focusing on the six most speciose subfamilies and considering all the ITR data published to date. The goal was to assess whether the presence, site number, and chromosomal location of ITRs convey any phylogenetic signal. We conducted fluorescent in situ hybridization (FISH) using an Arabidopsis-type telomeric sequence as a probe on karyotypes obtained from mitotic chromosomes. FISH signals of ITR sites were detected in species of subfamilies Asteroideae, Carduoideae, Cichorioideae, Gymnarhenoideae, and Mutisioideae, but not in Barnadesioideae. Although six small subfamilies have not yet been sampled, altogether, our results suggest that the dynamics of ITR formation in Asteraceae cannot accurately trace the complex karyological evolution that occurred since the early diversification of this family. Thus, ITRs do not convey a reliable signal at deep or shallow phylogenetic levels and cannot help to delimitate taxonomic categories, a conclusion that might also hold for other important families such as Fabaceae.

Phylogenomics unravels the early diversification of fungi

Our understanding of the eukaryote tree of life is continually improving, although the branching events at some of the deepest nodes remain elusive. The fungi are an ancient group of eukaryotes with a wide range of morphologies, life-history strategies, and ecological roles. While several recent phylogenomic analyses have been shown to be a powerful tool for uncovering even earliest diversifications, no study has yet examined the entire tree of fungi using a taxonomically comprehensive data set and suitable models of evolution. Here, we assembled a data set of 299 proteins from all recognised fungal groups for which genomic/transcriptomic data were available and subjected this to a battery of analyses, including tree inferences using site-heterogeneous mixture models and the Multi-Species Coalescent model. Tree topology was highly congruent and well supported, and any incongruence was found to result from an inability of some frequently used evolutionary models to model fast-evolving and heterogeneous sites. Our results provide higher resolution among early-branching lineages than previous studies, and shed light on hitherto highly contested evolutionary origins of the major fungal groups.

Chloranthus genome provides insights into the early diversification of angiosperms

Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

Most extant angiosperms belong to Mesangiospermae, which comprises eudicots, monocots, magnoliids, Chloranthales and Ceratophyllales. However, phylogenetic relationships between these five lineages remain unclear. Here, we report the high-quality genome of a member of the Chloranthales lineage (Chloranthus sessilifolius). We detect only one whole genome duplication within this species and find that polyploidization events in different Mesangiospermae lineage are mutually independent. We also find that the members of all floral development-related gene lineages are present in C. sessilifolius despite its extremely simplified flower. The AP1 and PI genes, however, show a weak floral tissue-specialized expression. Our phylogenomic analyses suggest that Chloranthales and magnoliids are sister groups, and both are together sister to the clade comprising Ceratophyllales and eudicots, while the monocot lineage is sister to all other Mesangiospermae. Our findings suggest that in addition to hybridization, incomplete lineage sorting may largely account for phylogenetic inconsistencies between the observed gene trees.

Ovipositor and mouthparts in a fossil insect support a novel ecological role for early orthopterans in 300 million years old forests

A high portion of the earliest known insect fauna is composed of the so-called ‘lobeattid insects’, whose systematic affinities and role as foliage feeders remain debated. We investigated hundreds of samples of a new lobeattid species from the Xiaheyan locality using a combination of photographic techniques, including reflectance transforming imaging, geometric morphometrics, and biomechanics to document its morphology, and infer its phylogenetic position and ecological role. Ctenoptilus frequens sp. nov. possessed a sword-shaped ovipositor with valves interlocked by two ball-and-socket mechanisms, lacked jumping hind-legs, and certain wing venation features. This combination of characters unambiguously supports lobeattids as stem relatives of all living Orthoptera (crickets, grasshoppers, katydids). Given the herein presented and other remains, it follows that this group experienced an early diversification and, additionally, occurred in high individual numbers. The ovipositor shape indicates that ground was the preferred substrate for eggs. Visible mouthparts made it possible to assess the efficiency of the mandibular food uptake system in comparison to a wide array of extant species. The new species was likely omnivorous which explains the paucity of external damage on contemporaneous plant foliage.

True hopper fossils (Fulgoromorpha and Cicadomorpha) in the Jurassic to Cretaceous of eastern Asia and their evolutionary implications

True hoppers, consisting of Fulgoromorpha and Cicadomorpha, are plant feeders with very high species-level diversity. A large amount of true hopper fossils have been reported from eastern Asia, especially from the Middle to Late Jurassic Yanliao Biota, the Early Cretaceous Jehol Biota and mid-Cretaceous Kachin amber in the last two decades. Herein, true hoppers from the Jurassic and Cretaceous of eastern Asia are reviewed, and combining palaeontological data from other regions of the world and recent advances of molecular studies, the evolutionary history of true hoppers in the mid-late Mesozoic is discussed. Permocicada beipiaoensis Wang, 1987 and Archijassus plurinervis Zhang, 1985 are here excluded from Prosboloidea and Archijassidae respectively. To the end of 2020, a total of 203 species with definite systematic position have been documented in the Jurassic and Cretaceous of eastern Asia (China, Myanmar, Siberia, Mongolia, Japan and Korea), and were attributed to 116 genera in 22 families and 7 superfamilies. Available fossil data suggest that true hopper components strongly changed in the Cretaceous: primitive groups reduced and went extinct successively, and the origin and/or early diversification of most lineages (family or subfamily level) occurred, likely owing to the displacement of host-plants in the angiosperm floristic revolution.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii are the most speciose living vertebrate clade, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches, and there is no comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. Past studies typically show low levels of diversity in the Devonian with a substantial rise in the early Carboniferous in the aftermath of the end-Devonian mass extinction. However there are unresolved patterns reported for the later Carboniferous and Permian. In large part, these conflicts span from a lack of publicly-available occurrence data: actinopterygians are majorly underrepresented in the Paleobiology Database (PBDB), for example, obscuring patterns of diversity through time. This is exacerbated by major taxonomic problems pervading the Palaeozoic actinopterygian record. Innumerable taxa are lumped into wide-ranging families and poorly-formulated genera, with a vast number of described species concentrated in several particularly problematic ‘waste-basket’ genera. This taxonomic confusion feeds into a limited understanding of phylogenetic relationships. There is also a heavy sampling bias towards Europe and North America, with other regions underrepresented despite yielding important occurrences. Scrutiny of the extent to which spatial biases influence the record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effect of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway to both redescribe poorly defined taxa and describe taxa from underrepresented regions, helping address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity from those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Evolution of andrenine bees reveals a long and complex history of faunal interchanges between the Americas during the Mesozoic and Cenozoic

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Among the main groups of bees, Andreninae sensu lato comprise about 3000 species widely distributed with greatest and disjunct diversity in arid areas of North America, South America, and the Palearctic region. Here, we present the first comprehensive dated phylogeny and historical biogeographic analysis for andrenine bees, including representatives of all currently recognized tribes. Our analyses rely on a dataset of 106 taxa and 7952 aligned nucleotide positions from one mitochondrial and six nuclear loci. Andreninae is strongly supported as a monophyletic group and the recovered phylogeny corroborates the commonly recognized clades for the group. Thus, we propose a revised tribal classification that is congruent with our phylogenetic results. The time-calibrated phylogeny and ancestral range reconstructions of Andreninae reveal a fascinating evolutionary history with Gondwana patterns that are unlike those observed in other subfamilies of bees. Andreninae arose in South America during the Late Cretaceous around 90 Million years ago (Ma) and the origin of tribes occurred through a relatively long time-window from this age to the Miocene. The early evolution of the main lineages took place in South America until the beginning of Paleocene with North American fauna origin from it and Palearctic from North America as results of multiple lineage interchanges between these areas by long-distance dispersal or hopping through landmass chains. Overall, our analyses provide strong evidence of amphitropical distributional pattern currently observed in Andreninae in the American continent as result at least three periods of possible land connections between the two American landmasses, much prior to the Panama Isthmus closure. The andrenine lineages reached the Palearctic region through four dispersal events from North America during the Eocene, late Oligocene and early Miocene, most probably via the Thulean Bridge. The few lineages with Afrotropical distribution likely originated from a Palearctic ancestral in the Miocene around 10 Ma when these regions were contiguous, and the Sahara Desert was mostly vegetated making feasible the passage by several organisms. Incursions of andrenine bees to North America and then onto the Old World are chronological congruent with distinct periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been instrumental to resolving the suprafamilial backbone of the charadriiform tree, several higher-level relationships, including the monophyly of plovers (Charadriidae) and the phylogenetic positions of several monotypic families, have remained unclear. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 336 ingroup taxa (89\% of all extant species), 24 loci (15 mitochondrial and 9 nuclear), and 69 morphological characters. Using this phylogeny, we clarify the charadriiform evolutionary timeline by conducting a node-dating analysis based on a subset of 8 loci tested to be clock-like and 16 carefully selected, updated, and vetted fossil calibrations. Our concatenated, species-tree, and total-evidence analyses consistently support plover monophyly and are generally congruent with the topologies of previous studies, suggesting that the higher-level relationships among shorebirds are largely settled. However, several localized conflicts highlight areas of persistent uncertainty within the gulls (Laridae), true auks (Alcinae), and sandpipers (Scolopacidae). At shallower levels, our phylogenies reveal instances of genus-level nonmonophyly that suggest changes to currently accepted taxonomies. Our node-dating analyses consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades. However, age estimates for more recent divergences vary between different relaxed clock models, and we demonstrate that this variation can affect phylogeny-based macroevolutionary studies. Our findings demonstrate the impact of fossil calibration choice on the resulting divergence time estimates, and the sensitivity of diversification rate analyses to the modeling assumptions made in time tree inference.