Comparative analyses of eight complete plastid genomes of two hemiparasitic vines in the family Lauraceae.

is the sole genus of hemiparasitic vines (ca. 20 spp.) belonging to the Cassytheae tribe of the Lauraceae family.

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.

Motivation: Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites but millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate and fast phylogenetic inference of resolvable phylogenetic features.

The complete chloroplast genome and phylogenetic relationship of Apocynum pictum (Apocynaceae), a Central Asian shrub and second-class national protected species of western China.

Apocynum pictum of the dogbane family, Apocynaceae, is a perennial semi-shrub species of ecological, medicinal, and economic value. It is mainly distributed in semi-arid, saline-alkaline, and desert regions of Xinjiang, Qinghai, and Gansu of western China and adjacent regions from Kazakhstan and Mongolia. Here, we reported the complete chloroplast (cp) genome of A.

(Loranthaceae), a new species of mistletoe from Samar Island, Philippines.

Background: The extensive forests over limestone of the Samar Island Natural Park (SINP) on Samar Island, Philippines harbour a rich variety of unique species. In this contribution, we describe and illustrate a new Loranthaceous mistletoe, endemic to Samar Island named , representing the 12th member of the genus reported to the Philippines.

New Information: This new species is similar to (Merr.

TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.

Motivation: Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of SARS-CoV-2 strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites and millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate phylogenetic inference of resolvable phylogenetic features.

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic.

Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient.

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic.

We report the likely most recent common ancestor of SARS-CoV-2 - the coronavirus that causes COVID-19. This progenitor SARS-CoV-2 genome was recovered through a novel application and advancement of computational methods initially developed to reconstruct the mutational history of tumor cells in a patient. The progenitor differs from the earliest coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections.

Splitting the birdcatcher trees: re-establishment of and (Nyctaginaceae, Pisonieae).

Several genera of Nyctaginaceae, currently merged under , have been described for the Indo-Pacific region. Results from a recent molecular phylogenetic study of tribe Pisonieae showed that is non-monophyletic and comprises three well-supported lineages: one including typical and allies ( s.str.

Two new species of (Viscaceae) from the Venezuelan Andes.

Two new species of Eichler (Viscaceae) from northwestern Venezuela are described and illustrated. Both mistletoes, Canelón et al., and Canelón et al.

A distinctive new species of flowerpecker (Passeriformes: Dicaeidae) from Borneo.

The enigmatic 'Spectacled Flowerpecker'-a probable new bird species from the island of Borneo-was first sighted in the Danum Valley of Sabah, Malaysia in 2009. However, the absence of a holotype specimen has prevented its formal scientific description. Since then only a handful of reports from widely disparate localities across the island have emerged, all from lowland sites and often in close association with fruiting mistletoe.

Agathis trees of Patagonia's Cretaceous-Paleogene death landscapes and their evolutionary significance.

Premise Of The Study: The fossil record of Agathis historically has been restricted to Australasia. Recently described fossils from the Eocene of Patagonian Argentina showed a broader distribution than found previously, which is reinforced here with a new early Paleocene Agathis species from Patagonia. No previous phylogenetic analyses have included fossil Agathis species.

Two new endemic tree species from Puerto Rico: and (Nyctaginaceae).

In this paper, we describe two endemic tree species of (Caryophyllales: Nyctaginaceae) from Puerto Rico that were erroneously catalogued under the single name Pisonia subcordata var. typica f. gigantophylla, misidentified as or , and informally named as "" and "".

Genetic Structure of the Bacterial Endosymbiont Buchnera aphidicola from Its Host Aphid Schlechtendalia chinensis and Evolutionary Implications.

Buchnera aphidicola is a primary symbiotic bacterium which provides essential amino acids to aphids. In this study, we sequenced nuclear 16s rDNA and atpAGD genes for 156 individuals of B. aphidicola from eight geographically distant populations to investigate the genetic diversity and structure of B.