A targeted NGS strategy using the Swift RNA Library Kit with the myBaits Expert Virus SARS-CoV-2 panel from Daicel Arbor Biosciences.

Rhodnius pallescens is the principal vector of Chagas disease in Panama. Recently a dark chromatic morph has been discovered in the highlands of Veraguas Province. Limited genetic studies have been conducted with regards to the population structure and dispersal potential of Triatominae vectors, particularly in R. pallescens. Next generation sequencing methods such as RADseq and complete mitochondrial DNA (mtDNA) genome sequencing have great potential for examining vector biology across space and time. Here we utilize a RADseq method (3RAD), along with complete mtDNA sequencing, to examine the population structure of the two chromatic morpho types of R. pallescens in Panama. We sequenced 105 R. pallescens samples from five localities in Panama. We generated a 2216 SNP dataset and 6 complete mtDNA genomes. RADseq showed significant differentiation among the five localities (FCT = 0.695; P = .004), but most of this was between localities with the dark vs. light chromatic morphs (Veraguas vs. Panama Oeste). The mtDNA genomes showed a 97–98% similarity between dark and light chromatic morphs across all genes and a 502 bp insert in light morphs. Thus, both the RADseq and mtDNA data showed highly differentiated clades with essentially no gene flow between the dark and light chromatic morphs from Veraguas and central Panama respectively. We discuss the growing evidence showing clear distinctions between these two morpho types with the possibility that these are separate species, an area of research that requires further investigation. Finally, we discuss the cost-effectiveness of 3RAD which is a third of the cost compared to other RADseq methods used recently in Chagas disease vector research.

There is an erratum for this article at: https://doi.org/10.1600/036364420X15959578652451 Abstract— Antennaria are dioecious perennial herbs distributed mainly in the Holarctic Region, with their major center of diversity in the Rocky Mountains of Western North America. The genus comprises 33 known sexual diploid/tetraploid species and at least five polyploid agamic complexes which mostly reproduce by forming asexual seeds. We performed a phylogenetic reconstruction of the 31 sexually-reproducing Antennaria species using a novel target enrichment method that employs custom capture probes designed to work across Asteraceae. Both concatenated and coalescent-based analyses of DNA sequence data from hundreds of nuclear loci recovered Antennaria as a monophyletic group except for the long-disputed species, Antennaria linearifolia , which was recovered outside of the genus. Antennaria was further resolved into three distinct, major lineages. Analysis of ancestral state reconstruction of 12 taxonomically important morphological characters elucidated patterns of character evolution throughout the genus. Estimations of ancestral geographic ranges and molecular dating analyses demonstrated the Rocky Mountain region, including the Vancouverian Province, as the center of origin for the genus Antennaria, around 5.8 MYA. Subsequent dispersals of Antennaria into the Arctic and Appalachian provinces, Canadian provinces, and Eurasia took place roughly 3.2 MYA, 2.4 MYA, and 1.6 MYA, respectively. Biogeographical stochastic mapping indicated that 51.4% of biogeographical events were based on within-area speciation. The remaining 48.6% of the events were divided into two types of dispersals: 1) range expansion dispersals (anagenic, 37%), and 2) founder/jump dispersals (cladogenic, 11.6%). Our results provide a framework for future evolutionary studies of Antennaria, including speciation, origin(s) of polyploidy, and agamospermy in the genus.

Treponema pallidum infections have been primarily known as slightly contagious mucocutaneous infections called yaws (tropical Africa and America) and bejel (subtropical North Africa). T. pallidum emerged as a highly infectious venereal syphilis agent in South America, probably about 500 years ago, and because of its venereal transmission, it quickly caused a worldwide pandemic. The disease manifests as lesions, including a chancre; then antibodies become detectable when or slightly after the chancre appears, and before the development of a rash and other systemic manifestations. Venereal diseases are poorly known in monkeys. During fieldwork in Senegal, we discovered an epizootic outbreak of venereal disease that we explored. We detected a venereal form of T. pallidum subsp. pertenue infection in green monkeys (Chlorocebus sabaeus), then observed an epizootic outbreak in Senegal and its spread among baboons a year later. Comparative analysis of T. pallidum genomes from the monkeys’ chancres and other Treponema genomes showed an acceleration of the number of single nucleotide polymorphisms, comparable to that observed in syphilis. Identified T. pallidum clones seem to be epizootic through the acceleration of their mutation rate, which is linked to their larger diffusion.

The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribe Aillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Attulus Simon, 1868, consisting of the subgenera Sitticus Simon, 1901 (seven described species), Attulus (41 described species), and Sittilong Prószyński, 2017 (one species). Five species of Attulus occur natively in North America, presumably through dispersals back from the Eurasian radiation, but an additional three species were more recently introduced from Eurasia. Attus palustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrys floricola C. L. Koch, 1837 (not a distinct subspecies). Attus sylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticus magnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulus floricola , A. sylvestris , A. cutleri , A. striatus , and A. finschi . The other sitticines of Canada and the U.S.A. are placed in separate genera, all of which arose from a Neotropical radiation including Jollas Simon, 1901 and Tomis F.O.Pickard-Cambridge, 1901: (1) Attinella Banks, 1905 ( A. dorsata , A. concolor , A. juniperi ), (2) Tomis ( T. welchi ), and (3) Sittisax Prószyński, 2017 ( S. ranieri ). All Neotropical and Caribbean “ Sitticus ” are transferred to either Jollas (12 species total) or Tomis (14 species). Attinella (three species) and Tomis are both removed from synonymy with Sitticus ; the synonymy of Sitticus cabellensis Prószyński, 1971 with Pseudattulus kratochvili Caporiacco, 1947 is restored; Pseudattulus Caporiacco, 1947 is synonymized with Tomis . Six generic names are newly synonymized with Attulus and one with Attinella . Two Neotropical species are described as new, Jollas cupreus sp. nov. and Tomis manabita sp. nov. Forty-six new combinations are established and three are restored. Three species synonymies are restored, one is new, and two are rejected. Across this diversity of species is a striking diversification of chromosome complements, with X-autosome fusions occurring at least four times to produce neo-Y sex chromosome systems (X 1 X 2 Y and X 1 X 2 X 3 Y), some of which ( Sittisax ranieri and S. saxicola ) are sufficiently derived as to no longer preserve the simple traces of ancestral X material. The correlated distribution of neo-Y and a base autosome number of 28 suggests that neo-Y origins occurred preferentially in lineages with the presence of an extra pair of autosomes.