Genome analysis suggests HTLV-1aA introduction in Chile related to migrations of ancestral indigenous populations.

The human T cell lymphotropic virus type 1 (HTLV-1), unlike other RNA viruses such as HIV, has a stable genome and has infected humans since remote times. Although the HTLV-1 infection is endemic in South America, there is scarce information about HTLV-1 in Chile and its history of introduction. This study assessed the genomic content of HTLV-1 from Chile and its relationship with HTLV-1 lineages circulating worldwide by phylogenetic reconstruction and dating analyses. A total of 30 HTLV-1 genomes collected from the four continents were used to conduct dating analyses, including the first HTLV-1 genome from Amerindian/Mapuche ethnicity. Estimation was performed using a Bayesian Markov Chain Monte Carlo coalescent-based approach as implemented in the BEAST program. The time of the most recent ancestor of HTLV-1 from Chile was ∼1409 years ago, which coincides with the period of Amerindian population expansion across South America. Our results suggest HTLV-1aA was possibly introduced in Chile during the migrations of the ancestral indigenous populations.

Systematics, biogeography, and character evolution of Deutzia (Hydrangeaceae) inferred from nuclear and chloroplast DNA sequences.

The genus Deutzia (Hydrangeaceae), containing ca. 60 species circumscribed in three sections, is disjunctly distributed in eastern Asia and Central America (Mexico). Although the genus is well delimited, its subdivisions into sections and series have not been the subject of an explicit test of monophyly based on molecular data. A comprehensive examination of the evolutionary relationships within the genus is thus still lacking. We present a fossil-calibrated, molecular phylogeny of Deutzia based on two nuclear ribosomal DNA (ITS and 26S) and three chloroplast DNA regions (matK, rbcL, and trnL-F intergenic spacer). Within this framework, we examine character evolution in petal arrangement, filament shape, and the number of stamens, and infer the ancestral area and biogeographic history of the genus. Our molecular phylogeny suggests that Deutzia is monophyletic. Two major clades are recovered: one composed of the species of sect. Neodeutzia from Mexico, and the other containing all remaining Deutzia species of sections Mesodeutzia and Deutzia from SW China and Northeast Asia. The latter two Asian sections were each revealed to be polyphyletic. The induplicate petals, 2-dentate filaments, and polystemonous androecia are inferred to be ancestral character states. Biogeographic reconstructions suggest a Northeast Asian origin for the genus and subsequent spread to Mexico during the Oligocene and to SW China during the Miocene. Based on our results, a new infrageneric classification of Deutzia inferred from molecular phylogeny is required. We propose to merge sections Mesodeutzia and Deutzia to ensure the monophyly at the sectional level. Cooling trends during the Oligocene resulted in isolation, separating eastern Asian and Mexican taxa, while the warm period during the middle Miocene stimulated the diversification from Northeast Asia to SW China. The uplift in the Qinghai-Tibetan Plateau and monsoon regimes are important in promoting high species diversification of Deutzia in SW China.

The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini).

Using complete mitochondrial genome sequences, we provide the first molecular analysis of the phylogenetic position of the yellow-tailed woolly monkey, Lagothrix flavicauda (a.k.a. Oreonax flavicauda), a critically endangered neotropical primate endemic to northern Perú. The taxonomic status and phylogenetic position of yellow-tailed woolly monkeys have been debated for many years, but in this study both Bayesian and maximum likelihood phylogenetic reconstructions unequivocally support a monophyletic woolly monkey clade that includes L. flavicauda as the basal taxon within the radiation. Bayesian dating analyses using several alternative calibrations suggest that the divergence of yellow-tailed woolly monkeys from other Lagothrix occurred in the Pleistocene, ∼2.1Ma, roughly 6.5 my after the divergence of woolly monkeys from their sister genus, Brachyteles. Additionally, comparative analysis of the cytochrome oxidase subunit 2 (COX2) gene shows that genetic distances between yellow-tailed woolly monkeys and other Lagothrix from across the genus' geographic distribution fall well within the range of between-species divergences seen in a large number of other platyrrhine primate genera at the same locus and outside the range of between-genus divergences. Our results thus confirm a position within Lagothrix for the yellow-tailed woolly monkey and strongly suggest that the name Oreonax be formally considered a synonym for this genus. This revision in taxonomic status does not change the dire conservation threats facing the yellow-tailed woolly monkey in Perú, where the remaining wild population is estimated at only ∼10,000 individuals living in a highly fragmented landscape.