When Roman administration and legions gradually withdrew from the outer provinces after the fall of the Western Roman Empire, they created a power voi…

Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum.To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus.The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered.This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ13C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs’ terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.

The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.

CRISPR technologies increasingly require spatiotemporal and dosage control of nuclease activity. One promising strategy involves linking nuclease activity to a cell’s transcriptional state by engineering guide RNAs (gRNAs) to function only after complexing with a ‘trigger’ RNA. However, standard gRNA switch designs do not allow independent selection of trigger and guide sequences, limiting gRNA switch application. Here, we demonstrate the modular design of Cas12a gRNA switches that decouples selection of these sequences. The 5 end of the Cas12a gRNA is fused to two distinct and nonoverlapping domains: one base pairs with the gRNA repeat, blocking formation of a hairpin required for Cas12a recognition; the other hybridizes to the RNA trigger, stimulating refolding of the gRNA repeat and subsequent gRNA-dependent Cas12a activity. Using a cell-free transcription-translation system and Escherichia coli, we show that designed gRNA switches can respond to different triggers and target different DNA sequences. Modulating the length and composition of the sensory domain altered gRNA switch performance. Finally, gRNA switches could be designed to sense endogenous RNAs expressed only under specific growth conditions, rendering Cas12a targeting activity dependent on cellular metabolism and stress. Our design framework thus further enables tethering of CRISPR activities to cellular states.

The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples.

Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

The Opiliones superfamily Triaenonychoidea currently includes two families, the monogeneric New Zealand–endemic Synthetonychiidae Forster, 1954 and Triaenonychidae Sørensen, 1886, a diverse family distributed mostly throughout the temperate Gondwanan terranes, with ~110 genera and ~500 species and subspecies currently described. Traditionally, Triaenonychidae has been divided into subfamilies diagnosed by very few morphological characters largely derived from the troublesome ‘Roewerian system’ of morphology, and classifications based on this system led to many complications. Recent research within Triaenonychoidea using morphology and traditional multilocus data has shown multiple deeply divergent lineages, non-monophyly of Triaenonychidae, and non-monophyly of subfamilies, necessitating a revision based on phylogenomic data. We used sequence capture of ultraconserved elements across 164 samples to create a 50% taxon occupancy matrix with 704 loci. Using phylogenomic and morphological examinations, we explored family-level relationships within Triaenonychoidea, including describing two new families: (1) Lomanellidae Mendes & Derkarabetian, fam. nov., consisting of Lomanella Pocock, 1903, and a newly described genus Abaddon Derkarabetian & Baker, gen. nov. with one species, A. despoliator Derkarabetian, sp. nov.; and (2) the elevation to family of Buemarinoidae Karaman, 2019, consisting of Buemarinoa Roewer, 1956, Fumontana Shear, 1977, Flavonuncia Lawrence, 1959, and a newly described genus Turonychus Derkarabetian, Prieto & Giribet, gen. nov., with one species, T. fadriquei Derkarabetian, Prieto & Giribet, sp. nov. With our dataset we also explored phylogenomic relationships within Triaenonychidae with an extensive taxon set including samples representing ~80% of the genus-level diversity. Based on our results we (1) discuss systematics of this family including the historical use of subfamilies, (2) reassess morphology in the context of our phylogeny, (3) hypothesise placement for all unsampled genera, (4) highlight lineages most in need of taxonomic revision, and (5) provide an updated species-level checklist. Aside from describing new taxa, our study provides the phylogenomic context necessary for future evolutionary and systematic research across this diverse lineage. ZooBank Registration: urn:lsid:zoobank.org:pub:81683834-98AB-43AA-B25A-C28C6A404F41

Genomic resources are under-developed for rodents, including well-studied species such as prairie dogs (Cynomys spp.). We conducted whole-genome resequencing on 10 Gunnison’s prairie dogs (C. gunnisoni, GUPD) and identified 12,842,055 high-quality SNPs, from which four sets of bait sequences were created. We designed two sets each (containing either 20k or 60k baits) for projects using contemporary (120 bp baits) or historical (100 bp baits) DNA. These bait sets can be used to study a variety of ecological and evolutionary questions in prairie dogs and other ground squirrel taxa.