Search Results (7)

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus Sassafras has long been controversial. Chloroplast (cp) evolution of Sassafras has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of Sassafras, and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 Sassafras ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (ccsA-ndhD, trnH-psbA, rps15-ycf1, and petA-psbJ) and 672 cp microsatellites were identified for Sassafras. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that Sassafras constituted a monophyletic clade and grouped a sister branch with the Cinnamomum sect. Camphora within the tribe Cinnamomeae. Divergence time between S. albidum and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), S. tzumu diverged from S. randaiense at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of Sassafras. Overall, our study clarified the evolution pattern of Sassafras cp genomes and elucidated the phylogenetic position and divergence time framework of Sassafras. Full article

The nocturnal, flightless camel crickets (Rhaphidophoridae) have a global distribution and are believed to have originated prior to the breakup of Pangea. We investigated the phylogeny and the timing of the radiation of East Asian species with mitogenomic data. Initially we analyzed a large taxon dataset (n = 117) using available partial mitochondrial and nuclear DNA sequences to confirm the monophyly of subfamilies and current taxonomy. Our findings support the monophyly of each genus within the subfamily Aemodogryllinae, with a minor inconsistency between taxonomy and phylogeny resolved by resurrection of the genus Gymnaeta Adelung. Fossil-calibrated molecular clock analysis used 11,124 bp alignment of 13 complete mitochondrial protein-coding genes for 20 species of Rhaphidophoridae, with a focus on the neglected Rhaphidophorinae and Aemodogryllinae lineages. Divergence time estimates suggest that the most recent common ancestor of the family lived during the Early Jurassic (189 Mya ± 23 Mya) before Pangea broke into the supercontinents or possibly during the early stage of breakup when Gondwana and Laurasia were still connected by land. The two subfamilies, Rhaphidophorinae and Aemodogryllinae, that overlap in Asia are estimated to have diverged 138 Mya ± 17 Mya, well before the Late Cretaceous northern connection between America and Asia (the Bering Land Bridge). Thus, our extended sampling of species from East Asia and Oceania refutes the importance of continental drift in the evolution of this wingless orthopteran family. Full article

Hawthorns (Crataegus L.) are widely distributed and well known for their medicinal properties and health benefits. Nevertheless, the phylogenetic relationships among Crataegus native to China remain unclear. Additionally, no consensus exists on the origin and evolution of Crataegus, and the relationship between Crataegus and Mespilus is is unclear. Here, we sequenced 20 chloroplast (cp) genomes (19 from Crataegus and 1 from Mespilus) and combined them with 2 existing cp genomes to investigate the phylogenetic relationships, divergence times and biogeographic history of Crataegus. Four hypervariable loci emerged from the newly sequenced genomes. The phylogenetic results indicated that the 14 Chinese Crataegus species analyzed clustered into two clades. One clade and the North American Crataegus species grouped together, while the other clade grouped with the European Crataegus species. Our results favor recognizing Mespilus and Crataegus as one genus. Molecular dating and biogeographic analyses showed that Crataegus originated in Southwest China during the early Oligocene, approximately 30.23 Ma ago. Transoceanic migration of East Asian Crataegus species across the Bering land bridge led to the development of North American species, whereas westward migration of the ancestors of C. songarica drove the formation of European species. C. cuneata may represent the earliest lineage of Chinese Crataegus. The uplift of the Qinghai–Tibet Plateau (QTP) and the Asian monsoon system may have led the ancestors of C. cuneata in south-western China to migrate toward the northeast, giving rise to other Chinese Crataegus species. This study offers crucial insights into the origins of Crataegus and proposes an evolutionary model for the genus. Full article

Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56–33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence. Full article

In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of ‘temporal signal dynamics’ along the phylogenetic tree. We showed that the evolutionary rate value of POWV is 3.3 × 10⁻⁵ nucleotide substitution per site per year (95% HPD, 2.0 × 10⁻⁵–4.7 × 10⁻⁵), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years. Full article

The timing of human entrance into North America has been a topic of debate that dates back to the late 19th century. Central to the modern discussion is not whether late Pleistocene-age populations were present on the continent, but the timing of their arrival. Key to the debate is the age of tools—bone rods, large prismatic stone blades, and bifacially chipped and fluted stone weapon tips—often found associated with the remains of late Pleistocene fauna. For decades, it was assumed that this techno-complex—termed “Clovis”—was left by the first humans in North America, who, by 11,000–12,000 years ago, made their way eastward across the Bering Land Bridge, or Beringia, and then turned south through a corridor that ran between the Cordilleran and Laurentide ice sheets, which blanketed the northern half of the continent. That scenario has been challenged by more-recent archaeological and archaeogenetic data that suggest populations entered North America as much as 15,300–14,300 years ago and moved south along the Pacific Coast and/or through the ice-free corridor, which apparently was open several thousand years earlier than initially thought. Evidence indicates that Clovis might date as early as 13,400 years ago, which means that it was not the first technology in North America. Given the lack of fluted projectile points in the Old World, it appears certain that the Clovis techno-complex, or at least major components of it, emerged in the New World. Full article

Ground-penetrating radar (GPR) offers many advantages for assessing archaeological potential in frozen and partially frozen contexts in high latitude and alpine regions. These settings pose several challenges for GPR, including extreme velocity changes at the interface of frozen and active layers, cryogenic patterns resulting in anomalies that can easily be mistaken for cultural features, and the difficulty in accessing sites and deploying equipment in remote settings. In this study we discuss some of these challenges while highlighting the potential for this method by describing recent successful investigations with GPR in the region. We draw on cases from Bering Land Bridge National Preserve, Cape Krusenstern National Monument, Kobuk Valley National Park, and Gates of the Arctic National Park and Preserve. The sites required small aircraft accessibility with light equipment loads and minimal personnel. The substrates we investigate include coastal saturated active layer over permafrost, interior well-drained active layer over permafrost, a frozen thermo-karst lake, and an alpine ice patch. These examples demonstrate that GPR is effective at mapping semi-subterranean house remains in several contexts, including houses with no surface manifestation. GPR is also shown to be effective at mapping anomalies from the skeletal remains of a late Pleistocene mammoth frozen in ice. The potential for using GPR in ice and snow patch archaeology, an area of increasing interest with global environmental change exposing new material each year, is also demonstrated. Full article